@article {pmid41212347,
year = {2025},
author = {Li, SW and Wang, HC and Chen, MS},
title = {Erianin is a therapeutic candidate for addressing neuroinflammation triggered by intracerebral hemorrhage.},
journal = {Langenbeck's archives of surgery},
volume = {411},
number = {1},
pages = {10},
pmid = {41212347},
issn = {1435-2451},
abstract = {BACKGROUND: Neuroinflammation is a common consequence of intracerebral hemorrhage (ICH), leading to neurological impairments. Research indicates that the gut microbiome can influence neuroinflammatory responses. Erianin, is a potential therapeutic agent in the treatment of inflammation. Yet, the specific impact of erianin on ICH-induced inflammation and its interaction with the gut microbiome remain areas of ongoing investigation.

METHODS: ICH mouse model was established and treated with erianin. Neurobehavioral tests, brain water content, immunofluorescence, western blotting, and terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining were performed to measure the neurological defects and neuroinflammation and neuron apoptosis. Immunofluorescent staining and western blotting assay were performed to assess the activation states of microglia and inflammation. The quantitative real-time polymerase chain reaction (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), and FITC-dextran assays were utilized to measure the intestinal barrier integrity. The composition of the gut microbiota was analyzed by sequencing the 16 S rRNA extracted from fecal samples.

RESULTS: Administration of Erianin notably decreased inflammation in the brain and improved neurological function in ICH mice by inhibiting the proinflammatory activation of microglia. Additionally, Erianin bolstered intestinal barrier integrity, evidenced by decreased levels of lipopolysaccharide-binding protein. Furthermore, treatment with Erianin led to observable shifts in the gut microbiota. Notably, the activation of the ERK signaling pathway was found to counteract the neuroprotective effects of Erianin following ICH.

CONCLUSIONS: Erianin is a therapeutic candidate for addressing neuroinflammation triggered by ICH, with its mechanisms of action likely involving the modulation of ERK signaling and the gut microbiome.},
}

@article {pmid41212059,
year = {2025},
author = {Vladar, EK and Gillen, AE and Yadav, S and Murphree, MR and Baraghoshi, D and Harris, JK and Pruesse, E and Niemiec, SS and Wilson, AW and Hisert, KB and Humphries, SM and Strand, M and Lynch, DA and Seibold, MA and Beswick, DM and Taylor-Cousar, JL},
title = {Transcriptomic and functional responses of the cystic fibrosis airway epithelium to CFTR modulator therapy.},
journal = {JCI insight},
volume = {10},
number = {21},
pages = {},
doi = {10.1172/jci.insight.196018},
pmid = {41212059},
issn = {2379-3708},
abstract = {Elexacaftor/tezacaftor/ivacaftor (ETI) cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to rapid and substantial improvements in cystic fibrosis (CF) airway disease. Underlying molecular and cellular mechanisms, long-term efficacy, and ability to reverse airway epithelial remodeling in established disease remain unclear. Longitudinal nasal brushes from an adult CF cohort were used to evaluate gene expression, cellular composition, stem cell function, and microbiome changes at baseline and at 6 months and 2 years after ETI. The baseline to 6 month span showed a massive downregulation of extensive neutrophilic inflammatory gene expression programs that correlated with increased pulmonary function and decreased sinusitis. Primary airway epithelial stem cell cultures from matched donor samples showed partially improved differentiation and barrier capacity at 6 months. Although clinical outcomes remained stable during the 6 month to 2 year span, transcriptional changes revealed a resurgence of baseline inflammatory programs. The time course of gene expression was consistent with ongoing normalization of epithelial remodeling. Relative abundance of Pseudomonas also decreased during the time course. These data suggest that ETI rectifies inflammation, epithelial remodeling, and bacterial infection in the airways, but resurgence of inflammatory gene expression may indicate ongoing inflammation, potentially presaging disease progression with long-term therapy.},
}

@article {pmid41212006,
year = {2025},
author = {Alshevskaya, AA and Aksenova, EI and Khasanov, RY},
title = {[Thematic priorities in oncology: analytical overview of publication trends and vectors of translational growth].},
journal = {Problemy sotsial'noi gigieny, zdravookhraneniia i istorii meditsiny},
volume = {33},
number = {0},
pages = {1069-1074},
doi = {10.32687/0869-866X-2025-33-s2-1069-1074},
pmid = {41212006},
issn = {0869-866X},
abstract = {Amid the rapid expansion of biomedical publications and the increasing complexity of the oncology research landscape, there is a growing need for a systematic analysis of thematic priorities that define global and national trajectories of scientific advancement. Oncology, as a field at the forefront of interdisciplinary innovation, spans domains from immune and cellular technologies to molecular imaging and epigenetic targets. Identifying frontier research areas that combine high scientific intensity, sustained international relevance, and translational potential is becoming a key tool for science policy and strategic planning. This study aims to map the most prominent oncology-related topics that emerged between 2021 and 2025, using data from the SciVal platform. A content-bibliometric analysis was conducted on the twenty leading thematic clusters in global oncology, followed by a comparative assessment of their representation in the Russian publication landscape. Metrics analyzed included publication output, field-weighted citation impact (FWCI), engagement dynamics, and institutional distribution. The results indicate that Russian research is contributing to several key topics, exhibiting high citation performance in niche areas such as exosomes, CAR-T therapy, radiomics, and immunotherapy for non-small cell lung cancer. However, many globally significant topics remain underrepresented in the Russian agenda, reflecting structural and human resource gaps in areas such as epigenetics, microbiome studies, precision immunomodulation, and regulated cell death mechanisms. These findings highlight both thematic gaps and institutional growth zones that require targeted support. Identifying advanced research areas positioned at the interface of scientific innovation and clinical applicability may inform the modernization of research infrastructure, the prioritization of national grant programs, and the integration of Russian research centers into global scientific consortia.},
}

@article {pmid41211992,
year = {2025},
author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y},
title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0163724},
doi = {10.1128/jvi.01637-24},
pmid = {41211992},
issn = {1098-5514},
abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.},
}

@article {pmid41211986,
year = {2025},
author = {Huang, Y and Wan, J and Shu, C and Yan, X and Ma, J and Zhang, T and He, J and Wan, Z and Li, G and Zhang, Q and Zhou, Z and Sun, X and Zhao, J and Zhang, P and Wang, L and Zhang, T and Tian, Q},
title = {Impact of oral Chlamydia vaccination on host gut microbiome and metabolite composition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0128525},
doi = {10.1128/msystems.01285-25},
pmid = {41211986},
issn = {2379-5077},
abstract = {Chlamydia trachomatis, an intracellular pathogen, is recognized as the most common sexually transmitted bacterial infection among women worldwide. Chlamydia infections can lead to undesirable clinical outcomes, including pelvic inflammatory disease and infertility. Recently, the gut has been identified as a niche for Chlamydia colonization in human gut-derived organoids. However, despite the biological impact on the host remaining under investigation, oral inoculation of Chlamydia as a whole-organism vaccine has been reported as a promising strategy for preventing genital Chlamydia infections in mice. Few studies have evaluated the impact of oral Chlamydia vaccination on the gut microbiome and metabolite changes. In this study, we assessed time-series alterations in the gut microbiome and metabolites following oral Chlamydia muridarum inoculation in a mice model, and we analyzed the composition and correlation between serum immune parameters and the sequencing profiles in the host. We identified 129 microbial changes and 186 differentially abundant metabolites in the gut across various vaccination approaches during the 30-day immunization process. Additionally, we discussed the potential influence of live Chlamydia on gut epithelium and the biomarkers of effective immunization based on correlation analysis.IMPORTANCEChlamydia infections primarily lead to morbidity rather than mortality. Consequently, in developing and implementing a Chlamydia vaccine, the utmost priority is evaluation of safety. As a promising yet controversial approach, live oral vaccination for Chlamydia raises concerns regarding its impact on the host's gut environment. Our study not only investigates changes in the gut microbiome and metabolites during vaccination but also identifies changes in gut epithelium during vaccination and potential biomarkers during immunization. These findings are crucial for the development of whole-organism oral Chlamydia vaccines and provide valuable insights into the long-term colonization of Chlamydia in the gut.},
}

@article {pmid41211985,
year = {2025},
author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O},
title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/msystems.01247-25},
pmid = {41211985},
issn = {2379-5077},
abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.},
}

@article {pmid41211636,
year = {2025},
author = {Wu, L and Zhang, Q and Tang, Z and Li, Y and Wu, T and Chen, L and Tan, C and Zhang, L and Ji, X and Zhang, S and Wu, Y and Bozec, A and Zaiss, MM and Luo, Y},
title = {Gut microbiota-derived tryptophan indole metabolites ameliorate collagen-induced arthritis in mice via aryl hydrocarbon receptor activation in T cells and intestinal epithelial cells.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.43430},
pmid = {41211636},
issn = {2326-5205},
abstract = {OBJECTIVE: To investigate the specific role of tryptophan metabolism, especially that of microbiome-derived metabolites, in the development of rheumatoid arthritis (RA).

METHODS: We employed metabolomics to profile metabolites in 53 high-risk for RA individuals (PreRAs), 30 established RA patients and 38 healthy individuals. Fecal microbiota transplantation (FMT) and collagen-induced arthritis (CIA) mouse models were used to investigate the impact of gut microbiome on arthritis severity, gut barrier function, and metabolic change. Treg cell differentiation and epithelial cells' barrier function were assessed by flow cytometry, immunofluoresence staining and western blotting. Co-immunoprecipitation and luciferase were applied for molecular mechanism studies.

RESULTS: Dysregulated tryptophan metabolism exists in RA and PreRA individuals, as well as in FMT mice, characterized by a shift toward the kynurenine pathway and reduced activity of serotonin and indole pathways. Indole-3-lactic acid (ILA) and indole-3-acetic acid (IAA) significantly alleviated arthritis in CIA mice by expanding Treg cells via the classical aryl hydrocarbon receptor (AhR)-aryl hydrocarbon receptor nuclear translocator (ARNT)-xenobiotic response element (XRE) signaling pathway. Moreover, ILA repaired the leaking gut by increasing Zo-1 and occludin expression in Caco-2 cells, which was blocked by AhR antagonist CH223191. Moreover, CH223191 treatment could significantly reverse the improving effects of ILA and IAA on arthritis in mice.

CONCLUSION: These findings indicate that Trp indole metabolites may play a negative regulatory role in the progression of RA by affecting Treg cell development and intestinal gut barrier function.},
}

@article {pmid41211602,
year = {2025},
author = {Wei, K and Yang, Y and Chen, C and Yang, Y and Hu, K and Chen, Q},
title = {Polypharmacy, anticholinergic burden and oral microbiome among U.S. middle-aged and older adults: a representative national survey.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2580559},
pmid = {41211602},
issn = {2000-2297},
abstract = {OBJECTIVES: Polypharmacy has been linked to alterations in gut microbiota, but its effects on the oral microbiome remain underexplored. This study aimed to examine the association of polypharmacy and anticholinergic burden with oral microbiome diversity and composition.

METHODS: We conducted a cross-sectional analysis using data from NHANES 2009-2012, including participants aged 55-69 years who reported at least one prescription medication. Polypharmacy was defined as the concurrent use of five or more medications. Anticholinergic burden was quantified by the Anticholinergic Cognitive Burden scale and the Anticholinergic Drug Scale. Oral microbiome profiling comprised alpha diversity, beta diversity, and taxonomic composition at multiple phylogenetic levels. Associations were analyzed via weighted multivariable linear regression, principal coordinate analysis (PCoA), and multivariate analysis of variance.

RESULTS: Among 1,596 participants, 29.2% reported polypharmacy, which correlated with higher anticholinergic burden. Both polypharmacy and anticholinergic burden were inversely associated with alpha diversity across multiple measures. Taxonomic analyses showed heterogeneous associations, with Porphyromonadaceae negatively linked to both exposures. PCoA indicated significant differences in community structure by polypharmacy status (Bray-Curtis: R² = 0.35%, P < .001).

CONCLUSIONS: Among middle-aged and older U.S. adults, both polypharmacy and anticholinergic burden were inversely associated with oral microbiome diversity and linked to distinct microbiome composition.},
}

@article {pmid41211554,
year = {2025},
author = {Gwon, H and Kim, HJ and Jeong, JW and Lee, D and Kim, JY and Shim, JJ and Lee, JH},
title = {Therapeutic potential of Codonopsis lanceolata peel extract in premenstrual syndrome: insights into hormonal, immune, and microbial interactions.},
journal = {Food science and biotechnology},
volume = {34},
number = {16},
pages = {4027-4038},
pmid = {41211554},
issn = {2092-6456},
abstract = {UNLABELLED: This study investigated the therapeutic potential of Codonopsis lanceolata peel extract (CPE) for premenstrual syndrome (PMS). The focus was on hormonal, immune, and microbial pathways. In vitro, CPE reduced nitric oxide production and suppressed IL-6 and TNF-α expression in LPS-stimulated macrophages. In pituitary GH3 cells stimulated with estradiol, CPE inhibited prolactin secretion. In a metoclopramide (MCP)-induced hyperprolactinemia mouse model, CPE decreased serum prolactin, PGE2, and inflammatory cytokines, while increasing PGE1 and FSH levels. Microbiome analysis showed that CPE enriched beneficial genera such as Lactobacillus and Bifidobacterium and reduced pro-inflammatory taxa including Oscillibacter and Desulfovibrionaceae. These microbial shifts were associated with improved inflammatory and hormonal markers. Overall, these findings suggest that CPE alleviates PMS symptoms by modulating endocrine function and regulating gut microbiota.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-025-02003-w.},
}

@article {pmid41211371,
year = {2025},
author = {Fang, L and Herrera-Herrera, A and Harris-Ricardo, J and Olier-Castillo, D and Fortich-Mesa, N and Hoyos-Hoyos, V},
title = {Exploring the Oral Microbiome in the Dental Biofilm of Children with Caries from Vulnerable Communities in Cartagena, Colombia: A Cross-sectional Study.},
journal = {International journal of clinical pediatric dentistry},
volume = {18},
number = {10},
pages = {1211-1216},
pmid = {41211371},
issn = {0974-7052},
abstract = {AIMS AND BACKGROUND: To explore the oral microbiome in the cariogenic dental biofilm in children from vulnerable communities in Cartagena, Colombia.

MATERIALS AND METHODS: We conducted a prevalence study that included 75 children aged 5-8 from three vulnerable communities in Cartagena, Colombia. Taking into account the International Caries Detection and Assessment System (ICDAS), calibrated examiners diagnosed all participants with dental caries. Samples of dental biofilm were obtained from carious tooth surfaces; extraction of bacterial DNA (deoxyribonucleic acid) was performed, and sequenced V3-V4 region of 16S rRNA (ribosomal ribonucleic acid) gene. Statistical analyses were conducted at the genus and species levels. Microbial diversity was analyzed using the Shannon diversity index.

RESULTS: The most prevalent bacterial genera identified were Streptococcus (probe 4), Lactobacillus (probe 5), Streptococcus (probe 1), and Fusobacterium (probe 4). The most abundant species identified were Lactobacillus salivarius, Streptococcus mutans, Streptococcus sanguinis, and Leptotrichia sp. HOT 417. A comparison of relative species abundance showed a more significant presence of Parascardovia denticolens, S. mutans, and Streptococcus sobrinus in extensive cavitated carious lesions (p < 0.001). The oral biofilm exhibited richness in bacterial species, as the α-Shannon index of 3.02 (SD 0.36) indicated.

CONCLUSION: The oral microbiome in the cariogenic dental biofilm in children from vulnerable communities in Cartagena shows high bacterial diversity, with specific species significantly associated with extensive cavitated lesions.

CLINICAL SIGNIFICANCE: Understanding the microbial diversity and specific bacterial associations in carious lesions provides valuable insights for developing targeted preventive and therapeutic strategies.

HOW TO CITE THIS ARTICLE: Fang L, Herrera-Herrera A, Harris-Ricardo J, et al. Exploring the Oral Microbiome in the Dental Biofilm of Children with Caries from Vulnerable Communities in Cartagena, Colombia: A Cross-sectional Study. Int J Clin Pediatr Dent 2025;18(10):1211-1216.},
}

@article {pmid41211322,
year = {2025},
author = {Pires, CP and Villela, LB and Moura, RL and Salomon, PS and Silva-Lima, AW},
title = {Hidden microalgae diversity in reef systems: reanalysis of coral microbiomes reveals spatial patterns of coral-associated plastid communities in the Southwestern Atlantic Ocean (SWAO).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20116},
pmid = {41211322},
issn = {2167-8359},
abstract = {The microbial community associated with corals plays a critical role in reef ecosystems, yet studies mainly focus on prokaryotes and Symbiodiniaceae, overlooking other oxygen-evolving photosynthetic eukaryotes. This leaves a knowledge gap regarding potentially important microbiome members. Here, we revisited coral microbiome datasets to investigate the diversity of plastid-bearing eukaryotes associated with Southwestern Atlantic Ocean (SWAO) corals. We compiled an inventory of plastid-bearing communities, uncovering their diversity and exploring ecological patterns. We further applied this approach to analyze the plastidiomes (plastid-bearing communities) of corals from the Abrolhos Bank, the largest reef system in the region, as a case study. A systematic literature review of 16S rDNA-based coral microbiome was conducted, excluding studies lacking plastid 16S sequences. The search made in PubMed resulted in 19 studies reporting corals sampled from 2009 to 2022, which were compiled and reanalyzed. Sequences of chloroplast origin (Silva 132) were further taxonomically classified by consensus-BLASTn search with the PR2 plastid 16S database. The dataset encompassed reef water and coral microbiomes from eight coral species, emphasizing the genus Mussismilia. A total of 272 amplicon libraries yielded 707,949 plastid sequences, identifying 196 algal genera across 41 classes. Reef water and coral plastid communities differed markedly. Ostreobium (81%) and Calliarthron (49%) were the most prevalent genera in coral samples. Diatoms were common (>40% of samples) in the water and in corals, whereas corallicolids were exclusive to corals (31.8%). The Abrolhos case study revealed geographic variation in Mussismilia harttii plastidiomes, which were less diverse than those in the water column. Coral indicator taxa included Ostreobium, corallicolids, Navicula, and Amphora. Our findings identify plastidiome variations and their implications for the coral host. Lipid-rich diatoms prevalent in coral plastidiomes may support corals nutritionally after coral bleaching, while other free-living and bloom-forming microalgae produce significantly more reactive oxygen species than Symbiodiniaceae, potentially driving oxidative stress. These results highlight microeukaryotic community variation across corals and its ecological relevance, offering a framework for using plastid-bearing communities as biomarkers of shifts in coral holobionts.},
}

@article {pmid41211308,
year = {2025},
author = {Delitte, M and Dubois, B and Morandini, L and Bultreys, A and Mahillon, J and Debode, F and Bragard, C},
title = {Biocontrol-relevant diversity of wheat-associated Pseudomonas: prevalence of P. sivasensis and identification of the novel species P. arvensis sp. nov.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20177},
pmid = {41211308},
issn = {2167-8359},
abstract = {The role of microbial communities in plant health and productivity has become increasingly evident. In this study, we investigated the diversity and functional potential of Pseudomonas spp. associated with Belgian cereal crops, focusing on wheat and spelt. From 444 Pseudomonas isolates, we identified 11 species, with several strains exhibiting strong antagonistic activity against major wheat pathogens. Notably, we report the high prevalence and efficient colonization abilities of Pseudomonas sivasensis, including its capacity to translocate from seed to leaf and suppress Zymoseptoria tritici infection in planta. Furthermore, we describe Pseudomonas arvensis sp. nov., a newly characterized species within the wheat microbiome, with DR1PS3 designated as the type strain. Our results advance the understanding of beneficial plant-microbe interactions in cereals and highlight the promise of native Pseudomonas species as biocontrol agents for sustainable disease management.},
}

@article {pmid41210947,
year = {2025},
author = {Negut, I and Mazzanti, C and Laurano, R and Ciardelli, G and Bronco, S and Oliveira, CS},
title = {From 1D microbiological assays to 3D advanced skin models: enhancing preclinical strategies to unravel the impact of bioactive textiles on the human skin microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1676663},
pmid = {41210947},
issn = {2235-2988},
abstract = {Bioactive textiles have emerged as multifunctional materials to actively interact with the human skin and its microbiome. By embedding natural or synthetic bioactive compounds, such as chitosan, essential oils, plant extracts, and metallic nanoparticles, these materials aim to prevent and target infections, modulate inflammation, and promote skin homeostasis. Given the critical role of the skin microbiome in maintaining barrier integrity and immune balance, strategies that selectively inhibit pathogenic microorganisms (e.g., Staphylococcus aureus, Cutibacterium acnes) while preserving beneficial commensals like Staphylococcus epidermidis are essential to avoid dysbiosis and associated dermatological disorders. This review highlights current trends in the design and functionalization of bioactive textiles, emphasizing sustainable and biocompatible approaches that leverage natural antimicrobial compounds and green synthesis techniques. It also examines conventional evaluation pipelines primarily based on 1D microbiological assays and 2D skin models, highlighting their limitations in predicting real-world performance. Advanced in vitro models, particularly 3D reconstructed human skin platforms incorporating both pathogenic and commensal microbiota members, are presented as indispensable tools to study fabric-skin-microbe interactions under physiologically relevant conditions. These models enable accurate assessment of antimicrobial efficacy, biocompatibility, and microbiome impact, providing a bridge between in vitro and clinical outcomes. Furthermore, the potential of bioactive textiles in managing microbiome-related skin conditions, such as atopic dermatitis and acne, is discussed alongside the importance of developing microbiome-safe materials. Despite encouraging clinical evidence demonstrating pathogen reduction and symptomatic improvement, the successful translation of these materials to clinical practice needs interdisciplinary research and the adoption of advanced preclinical strategies to ensure innovative solutions for personalized skin health.},
}

@article {pmid41210709,
year = {2025},
author = {Hou, L and Han, B and Wang, Y and Wang, X and Shi, W and Cao, N and Zhang, Y},
title = {Microbial response to long-term spatially stratified phosphorus application in Northeast China.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1669876},
pmid = {41210709},
issn = {1664-462X},
abstract = {As a critical factor influencing crop productivity in agricultural ecosystems, phosphorus (P)-fertilizer application can significantly alter soil physicochemical properties. However, the relative efficiencies of different types of spatially stratified P fertilizers and their underlying biological mechanisms remain insufficiently elucidated. In this study, an 8-year field experiment was conducted in a black soil region of Northeast China to compare the effects of five P-fertilization regimes: CK (without P application), FP (100% as basal fertilizer), APP (20% as starter fertilization by ammonium polyphosphate), MAP (20% as starter fertilization by monoammonium phosphate), and CMP (20% as starter fertilization by calcium magnesium phosphate). We systematically investigated the effects of spatially stratified P fertilization on soil physical properties, nutrient accumulation, maize yield performance, and bacterial and fungal community structure. CMP demonstrated the best performance in improving soil aeration and enhancing water infiltration capacity. MAP significantly increased the soil total P content by 18.62% and the soil Olsen-P content by 81.46% compared to those of FP. Both MAP and CMP promoted P uptake in various parts of maize plants, including the roots, straw, and grains. All tested starter P fertilizers improved P use efficiency. Compared to that of FP, the soil P surplus was reduced by 7.52%, 14.74%, and 13.04% under APP, MAP, and CMP, respectively. MAP demonstrated the most pronounced yield-increasing effect. Based on amplicon sequencing (16S rRNA for bacteria, interspacer region for fungi) and microbiome profiling, this study confirms that fungi are more susceptible than bacteria to variations in fertilizer types and application methods. Furthermore, the relative abundance of Tausonia was most significantly influenced by MAP. By enhancing the relative abundance of P-cycling functional genes (gph, phoU), MAP modulated the abundance of dominant microbial taxa such as Acidobacteria and Proteobacteria, thereby significantly improving maize yield. Therefore, in maize cropping systems in the black soil region of Northeast China, optimized P fertilizer selection and application methods can effectively reduce soil P surplus and modulate microbial community structure and functional diversity while maintaining stable crop yields.},
}

@article {pmid41210228,
year = {2025},
author = {Huang, H and Ma, D and Zhou, Y and Wu, L},
title = {Effect of probiotics and related supplements on glycemic control in pediatric patients with type 1 diabetes mellitus: a systematic review and meta-analysis of clinical trials.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1633694},
pmid = {41210228},
issn = {2296-2360},
abstract = {OBJECTIVE: Type 1 diabetes mellitus (T1DM) is a common autoimmune disease in children, characterized by the destruction of pancreatic β-cells. Despite treatment advancements, many patients struggle with glycemic control. Recent research suggests the gut microbiome plays a role in T1DM, with dysbiosis contributing to its onset. Probiotics may help improve glycemic control and reduce inflammation, but their effects in children with T1DM are unclear. This study systematically reviews the impact of probiotics and related supplements on glycemic control in pediatric T1DM patients.

METHODS: This study adhered to PRISMA guidelines and was registered in PROSPERO (CRD42025633971). We searched databases including PubMed and EMBASE until January 5, 2025. The focus was on randomized controlled trials (RCTs) involving participants under 18 with T1DM, examining the effects of probiotics, prebiotics, and synbiotics on glycemic control indexes like fasting blood glucose (FBG), hemoglobin A1c (HbA1c), C-peptide, and insulin needs. Two researcher extracted data, quality was assessed via the Cochrane Handbook, and STATA 16 was used for statistical analysis.

RESULTS: Eight RCTs with 494 participants (246 intervention, 248 control) showed that probiotics and synbiotics significantly reduced HbA1c levels [Weighted Mean Difference (WMD) = -0.25%, 95% Confidence Interval (CI) = -0.45, -0.04; p = 0.019] with low heterogeneity [I-squared (I[2]) = 22%]. However, no significant changes were found in FBG, C-peptide levels, or insulin requirements. Sensitivity analyses yielded similar directions of effect for HbA1c. Subgroups suggested larger HbA1c reductions with longer intervention duration, shorter disease duration, and multi-strain formulations.

CONCLUSION: Probiotic supplementation may achieve a small improvement in HbA1c in pediatric T1DM. Adequate dosing, longer intervention duration, and multi-strain formulations may be more likely to improve HbA1c, but the clinical importance is uncertain. However, our result shows no significant effects on fasting blood glucose, C-peptide, or insulin requirements; no routine clinical recommendations are proposed. The role of probiotics and related supplements in long-term glycemic control still requires confirmation through trials with extended follow-up. Large-scale, rigorously designed studies are needed to determine optimal intervention parameters, clarify underlying mechanisms, and evaluate the clinical applicability of probiotics in T1DM management.

identifier [CRD42025633971].},
}

@article {pmid41209829,
year = {2025},
author = {Yang, M and Liu, Y and Xia, Y and Li, M and Huang, C and Hou, F and Hu, S and Zhu, X and Wang, M and Shi, J and Wan, R and Zhang, K and Hao, P and Zhao, Y and Liu, Y and Shen, Y and Cong, L and Han, Z and Feng, J and Jiao, J and Zheng, X},
title = {A synthetic microbial community derived from healthy apple rhizosphere alleviates apple replant disease.},
journal = {Horticulture research},
volume = {12},
number = {11},
pages = {uhaf217},
pmid = {41209829},
issn = {2662-6810},
abstract = {Apple replant disease (ARD) poses a major threat to global orchard productivity, yet its biological causes remain poorly understood. Although microbial dysbiosis in replant soils has been recognized as a major contributing factor, the specific pathogenic agents involved and the efficacy of synthetic microbial communities in mitigating ARD remain unclear. In this study, we integrated physiological, transcriptomic, metabolomic, and microbiome analyses to investigate the effects of replant soils on the growth of Malus domestica rootstock M26. Absolute quantification amplicon sequencing of 16S rRNA and ITS regions revealed a marked decline in rhizospheric microbial diversity in replant soils compared to fallow controls, accompanied by an enrichment of fungal genera such as Fusarium, Aspergillus, and Acremonium. Pathogenicity assays and seedling colonization experiments verified strong pathogenicity for five isolates-Acremonium sp., Aspergillus niger, Fusarium solani, Macrophomina phaseolina, and Aspergillus stellatus-implicating them as potential causal agents of ARD. High-throughput culturing and confrontation assays were used to isolate and screen candidate microbial antagonists. A synthetic microbiota (SynMs) composed of 12 bacterial strains and Trichoderma sp. was developed. Inoculation with SynMs significantly inproved plant height by 133% (P < 0.05) and total root length by 186% (P < 0.01), and effectively suppressed pathogen proliferation of the five pathogenic isolates in replant soils. Collectively, these findings identify key fungal pathogens underlying ARD and propose a sustainable microbiota-based strategy for its effective mitigation, offering both mechanistic insights and practical solutions for microbiome-informed orchard management.},
}

@article {pmid41209726,
year = {2025},
author = {Sun, Z and Huang, R and Chen, J and Song, Y and Sun, Z and Zhang, L and Shi, H and Mu, R and Wang, Y and Huang, J and Yan, X and Tan, Q},
title = {Androgen deprivation promotes diabetic wound healing in mice through modulation of wound microbiome and immune response.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684165},
pmid = {41209726},
issn = {1664-302X},
abstract = {INTRODUCTION: Delayed wound healing is a major complication of diabetes, often associated with chronic inflammation and microbial dysbiosis. Although androgens are known to impair wound repair, their role in diabetic wound healing, particularly in regulating the local wound microbiome and associated immune response, remains poorly understood. In this study, we investigated whether androgen deprivation via surgical castration could enhance diabetic wound healing by modulating local microbial communities and inflammation.

METHODS: A full-thickness wound model was established in db/db mice. Surgical castration was used to achieve androgen deprivation. Wound closure and histology were assessed longitudinally. Blood glucose and body weight were monitored. The local immune microenvironment was profiled, focusing on pro-inflammatory factors and macrophage polarization. 16S rRNA sequencing characterized α-diversity and community composition over time. Functional prediction analyses inferred microbial metabolic potential, and machine-learning models evaluated taxa associated with healing dynamics.

RESULTS: Androgen deprivation significantly accelerated wound closure and improved histological outcomes without altering blood glucose or body weight. The wound microenvironment showed reduced pro-inflammatory factors and enhanced M2 macrophage polarization. 16S rRNA sequencing revealed increased microbial α-diversity and durable shifts in community composition, most prominently during early healing. Escherichia-Shigella, Rhodococcus, and Ochrobactrum were enriched, while Staphylococcus abundance decreased. Functional prediction indicated elevated microbial metabolic activity after castration. Machine-learning analysis identified Escherichia-Shigella as a key genus associated with accelerated healing.

DISCUSSION: Low androgen levels were associated with improved diabetic wound repair, potentially by attenuating local inflammation and fostering a more diverse, metabolically active microbiota. These data support a mechanistic link among androgens, wound inflammation, and the microbiome, and suggest host-directed therapeutic strategies for chronic diabetic wounds.},
}

@article {pmid41209719,
year = {2025},
author = {Tufail, A and Bo, T and Zhao, N and Willows-Munro, S and Khan, BN and Duan, J and Jin, J and Qu, Y and Lei, F and Song, G},
title = {Exploring microbiome shifts across taxonomic and ecological groups of birds at a key stopover site in Punjab, Pakistan.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100492},
pmid = {41209719},
issn = {2666-5174},
abstract = {Birds are important vectors of microbial transmission across diverse habitats. yet their gut microbiome dynamics from South Asian migratory stopover sites remain poorly understood. This study presents the first comprehensive assessment of gut microbiome variation across avian ecological types during the late wintering period at the Ravi River Siphon, a stopover in Punjab, Pakistan. Using 16S rRNA gene sequencing, we profiled gut microbial characters of 41 bird individuals from 17 species representing seven avian orders. Alpha diversity differed significantly across both ecological types and taxonomic orders, while beta diversity showed overlapping communities, with limited group distinctions. Dominant phyla included Firmicutes, Proteobacteria, Actinobacteriota, Chloroflexi, and Bacteroidota, with notable group specific enrichments. LEfSe analysis identified five differentially abundant biomarker taxa across ecological types and seven orders, and PICRUSt2 based functional predictions revealed enrichment of pathways related to metabolism, immune function, and xenobiotic degradation, varying notably by ecological type/taxonomic orders. Importantly, we detected several potential zoonotic pathogens, including Enterococcus, Escherichia-Shigella, Acinetobacter, and Corynebacterium, highlighting the need for pathogen surveillance in avian populations. Our findings indicate that both ecology and host taxonomy are key determinants of avian gut microbiome composition, with taxonomic order showing a stronger influence on microbial structure. Together, these results provide the first region-specific baseline from a migratory stopover in Punjab, Pakistan, addressing a major geographic gap in avian microbiome research and offering essential data for future conservation and pathogen monitoring in dynamic wetland ecosystems.},
}

@article {pmid41209469,
year = {2025},
author = {Zhao, Z and Wei, X and Deng, F and Yang, S and Li, Y and Chai, J},
title = {Editorial: Advancements in synthetic microbiomes for enhancing animal health.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1708299},
pmid = {41209469},
issn = {2297-1769},
}

@article {pmid41209147,
year = {2025},
author = {Massey, WJ and Brown, JM},
title = {The role of metaorganismal lipid metabolism in human health and disease.},
journal = {Immunometabolism (Cobham, Surrey)},
volume = {7},
number = {4},
pages = {e00074},
pmid = {41209147},
issn = {2633-0407},
abstract = {Most chronic diseases including coronary heart disease, obesity, diabetes, cancer, and multiple neurodegenerative diseases are driven by dysregulated lipid metabolism. In fact, many common drugs taken by millions including aspirin, statins, fibrates, and others improve health by reorganizing systemic lipid metabolism. Although we have a wealth of information on the enzymes and pathways maintaining lipid metabolic homeostasis in our human cells, there is much less known in regard to how our gut microbiome may coordinate with the host to control systemic lipid metabolism. With advances in untargeted metabolomics, there is a rapidly expanding list of gut microbe-derived lipid metabolites with unannotated function. Many of these bacterial lipids can be assimilated into host lipids and alter host lipid metabolic processes. Here, we discuss how gut microbe-derived lipids may be further metabolized by the host through metaorganismal metabolic pathways. We also discuss the untapped therapeutic potential for targeting metaorganismal lipid metabolism for the improvement of human health.},
}

@article {pmid41209022,
year = {2025},
author = {Piednoir, A and Troussier, F and Descamps, M and Lagarce, L and Martin, L},
title = {Cutaneous and Ocular Rosacea Associated with Elexacaftor, Tezacaftor and Ivacaftor, A Treatment for Cystic Fibrosis: A Case Report.},
journal = {Journal of pediatrics. Clinical practice},
volume = {18},
number = {},
pages = {200187},
pmid = {41209022},
issn = {2950-5410},
abstract = {A 6-year-old girl with cystic fibrosis developed ocular and cutaneous rosacea after the initiation of elexacaftor-tezacaftor-ivacaftor therapy. Her symptoms improved upon discontinuation and recurred with reintroduction, suggesting a drug-induced reaction. This case suggests a potential, previously unreported association between elexacaftor-tezacaftor-ivacaftor and rosacea, possibly mediated by microbiome alterations and inflammation.},
}

@article {pmid41208900,
year = {2025},
author = {Yang, R and Yang, Y and Wu, L and He, K and Bi, D and Teng, L},
title = {Lactobacillus paracasei ZJUZ2-3 inhibits gastrointestinal tumors via the IAA-induced AHR/MTDH/NF-κB axis.},
journal = {International journal of biological sciences},
volume = {21},
number = {14},
pages = {6522-6541},
pmid = {41208900},
issn = {1449-2288},
abstract = {Lactobacillus paracasei abundance is markedly reduced in gastric cancer (GC) tissues, suggesting its potential protective role. From healthy gastric tissue of a GC patient, we isolated a novel strain, L. paracasei ZJUZ2-3, which exerted potent antitumor effects. Intratumoral injection of live ZJUZ2-3, but not heat-killed bacteria, attenuated gastrointestinal tumor growth in mice. Conditioned medium from ZJUZ2-3 similarly inhibited cancer cell proliferation, implicating a secreted metabolite. Metabolomic profiling identified indole-3-acetic acid (IAA) as the key bioactive compound. Consistent with this, genetic knockout of trpA (essential for IAA biosynthesis) in ZJUZ2-3 abolished its antitumor efficacy. IAA alone recapitulated the tumor-suppressive effects both in vitro and in vivo. Mechanistically, IAA activated the aryl hydrocarbon receptor (AHR), which then competitively bound to metadherin (MTDH). This interaction blocked MTDH phosphorylation and the subsequent activation of NF-κB signaling. Crucially, depletion of either AHR or MTDH abrogated IAA's efficacy, underscoring the essential role of this axis. Furthermore, ZJUZ2-3 synergized with conventional chemotherapy, potentiating tumor regression. While this study lacks humanized immune models and exploration of strain-specificity, our findings identify L. paracasei ZJUZ2-3 and its effector metabolite IAA as promising precision microbiome-based therapeutics targeting the AHR-MTDH-NF-κB pathway for adjuvant treatment of GC.},
}

@article {pmid41208872,
year = {2025},
author = {Sun, J and Chen, J and Shen, Y and Yao, X and Sun, H and Chen, B and Feng, J},
title = {Diabetes mellitus-driven pulmonary injury: multidimensional mechanisms linking metabolic dysregulation to gut-lung axis and promising therapies.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1689522},
pmid = {41208872},
issn = {1663-9812},
abstract = {Diabetes mellitus (DM), a globally prevalent metabolic disorder, poses a significant public health threat due to its systemic complications. Recent studies have increasingly recognized the lung as a target organ in diabetic pathology. However, owing to the respiratory system's complex physiology, the mechanisms underlying DM-associated lung injury remain poorly understood and require further investigation. This review systematically elucidates the multifaceted effects of DM-induced metabolic disturbances on the lung, with a focus on four key pathophysiological axes triggered by hyperglycemic homeostasis, including chronic inflammation, oxidative stress imbalance, endocrine network disruption, and intestinal dysbiosis. Building upon the "metabolism-microbiota-immune" axis framework, this study demonstrates that: persistent hyperglycemia induces pulmonary tissue damage and immune microenvironment disruption through metabolite accumulation and mitochondrial dysfunction; DM-associated intestinal dysbiosis amplifies pulmonary inflammation via the gut-lung axis, mediated by metabolic reprogramming and immune cell trafficking; and metabolic aberration-driven dysregulation of innate/adaptive immunity serves as the pivotal mediator for progressive lung injury. Building on this mechanistic framework, we discuss emerging therapeutic avenues that target metabolic reprogramming, modulation of the gut microbiota, and restoration of immune homeostasis. Promising strategies include repurposed antidiabetic drugs (e.g., SGLT-2 inhibitors, GLP-1 receptor agonists), microbiome-targeted therapies (e.g., fecal microbiota transplantation), and novel immunomodulatory agents. These therapies are offering a new shift towards multi-target treatments for diabetic pulmonary complications.},
}

@article {pmid41208518,
year = {2025},
author = {Yang, Y and Wen, L and Lin, W and Chen, Y and Yang, R and He, C and Zhang, Y and Zhang, J and Wang, H and Wang, H and Teng, L},
title = {Microbial and Metabolomic Variations Correlated With Gastric Cancer Subtypes and Prognosis.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70139},
doi = {10.1002/mbo3.70139},
pmid = {41208518},
issn = {2045-8827},
support = {//This study was supported by the National Natural Science Foundation of China (No. 82302886), the Project of the Regional Diagnosis and Treatment Centre of the Health Planning Committee (No. JBZX-201903), and the Department of Science and Technology of Zhejiang Province, "Pioneer" and "Leading Goose" R&D Program of Zhejiang, NO.2024C03146./ ; },
abstract = {Gastric cancer (GC) persists as the third most prevalent malignancy in China. GC exhibits distinct features when stratified by Lauren/ZJU subtypes. The interdependence of microbes, metabolites, and tumor evolution is recognized. Nevertheless, the specific microbial and metabolite disparities related to the Lauren and ZJU subtypes of GC have yet to be thoroughly investigated. In this study, we employed 16S sequencing of microbial communities and conducted untargeted metabolomic assessments on tumor tissues and their matched normal controls from 50 GC patients. We observed variations in microbial composition and metabolite landscapes across subtypes, irrespective of the Lauren or ZJU classification. We explored the associations and differences between the Lauren and the ZJU classification. It was found that both classifications share differential microbiota, including Fusobacterium and Haemophilus. Additionally, 38 of the top 50 differential metabolites are common to both classifications. However, distinct classifications also exhibit unique differential microbiota and metabolite characteristics. Among them, Eubacterium_ventriosum_group and N6-Succinyl Adenosine are both characteristic differences of the ZJU classification. Multivariate survival analysis disclosed that Eubacterium_ventriosum_group positively correlates with poor prognosis, whereas N6-Succinyl Adenosine negatively correlates with poor prognosis. Our research delineates the microbiota and metabolites specific to different subtypes of GC and investigates the interplay between these differential elements, as well as their prognostic significance. We have identified two distinct features that are both associated with the ZJU classification, suggesting that the ZJU classification is more closely related to prognosis.},
}

@article {pmid41208300,
year = {2025},
author = {Ma, Y and Yan, H and Abukhader, OS and Li, D and Zhang, S},
title = {Sublethal effects of matrine and azadirachtin on the wolf spider Pardosa laura: no impairment of growth but marked suppression of reproduction.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70347},
pmid = {41208300},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Plant-derived pesticides (PDPs) are increasingly promoted as 'eco-friendly' alternatives to agrochemicals because of their low vertebrate toxicity, yet their safety for non-target arthropod natural enemies is rarely tested, especially the enrichment effect via trophic transfer.

RESULTS: We cultured fruit flies using media supplemented with two widely applied Chinese PDPs in tea plantations, matrine or azadirachtin, under commercial concentration, which were fed to newly emerged spiderlings of wolf spider Pardosa laura (Araneae: Lycosidae) throughout their entire life cycle. We examined the effect of these two PDPs on their survival, developmental parameters and reproduction. The results showed that developmental traits remained unaffected, but both PDPs markedly suppressed male mating success and female fecundity. Histological examination of paraffin sections revealed markedly impaired ovarian maturation. Microbiome profiling indicated that pesticide exposure disrupted ovarian microbial communities, with azadirachtin exerting the strongest effect, whereas gut and testicular communities remained largely unchanged. Transcriptomic analysis of ovaries showed significant enrichment of pathways related to ovarian development. Ten representative differentially expressed genes (DEGs) within these pathways were selected and validated by RT-qPCR.

CONCLUSION: PDPs may not compromise the development of spiders in the first generation, yet they can severely affect reproduction of the spiders, thereby precipitating substantial declines in population size of future generations. This result challenges the conventional wisdom of botanical pesticides, inspiring re-consideration of their rational use in integrated pest management. © 2025 Society of Chemical Industry.},
}

@article {pmid41208257,
year = {2025},
author = {Dias Nirello, V and Araújo, N and Carvalho de Assis, H and Moreno-Gonzalez, M and Ruiz, P and Castro, PR and Shealy, NG and Shelton, C and Font Fernandes, M and de Oliveira, S and Boroni, M and Ryffel, B and Byndloss, MX and Beraza, N and Ramirez Vinolo, MA and Varga-Weisz, P},
title = {Microbiota shape the colon epithelium controlling inter-crypt absorptive goblet cells via butyrate-GP R109A signalling.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2573045},
doi = {10.1080/19490976.2025.2573045},
pmid = {41208257},
issn = {1949-0984},
abstract = {The colonic epithelium is a key interface between the gut microbiota and the host. How microbiota-derived signals influence epithelial cell identity and function remains incompletely understood. Here, we used single-cell transcriptomics, antibiotic-mediated microbiota depletion, germ-free mice and colonization experiments in mice to uncover cell-type-specific responses to microbiota changes, highlighting changes in the cell composition and functional diversities in enterocytes. Our analysis demonstrates that the microbiota control the absorptive profile of the colon epithelial cells and reveals non-canonical inter-crypt goblet cells as microbiota-responsive constituents that combine absorptive and secretory features and whose abundance is regulated by the gut microbiota. We found that their number is suppressed through the short-chain fatty acid butyrate and its receptor GPR109A. Analysis in mouse and humans indicates that the expansion of this hybrid population increases with age and that this expansion is driven by microbiome changes. Our work reveals a previously unrecognized level of epithelial plasticity driven by microbial triggers and highlights butyrate, acting as a signaling molecule that shapes the colon micro-anatomy.},
}

@article {pmid41208251,
year = {2025},
author = {Ding, M and Ross, RP and Dempsey, E and Li, B and Stanton, C},
title = {Infant gut microbiome reprogramming following introduction of solid foods (weaning).},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2571428},
doi = {10.1080/19490976.2025.2571428},
pmid = {41208251},
issn = {1949-0984},
abstract = {The infant gut microbiome undergoes a crucial transformation when solid foods enter the diet during weaning. This introduction normally happens at about six months post-birth and leads to major shifts in the gut microbiome. Many of the changes that occur during this period are known to persist into adulthood. While many perinatal factors, including gestational age, delivery mode, feeding choices, and antibiotic exposure, strongly influence microbiome composition and functional trajectories, the effects of weaning, in particular, have received far less attention. This review examines the response of the microbiome ecosystem when the diet is radically altered through the introduction of solid foods during the weaning phase. This response involves major reshaping of anabolic and catabolic functioning, along with changes in bacterial taxa and increased diversity. The information presented in this review aims to fill existing knowledge gaps while advancing our comprehension of how the infant diet shapes gut microbiome development through childhood.},
}

@article {pmid41207985,
year = {2025},
author = {Mei, J and Li, L and Ma, ZS},
title = {Unraveling the Ecological Mechanisms Influencing the Structure and Composition of Lung Cancer Microbiomes.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {119},
pmid = {41207985},
issn = {1432-184X},
abstract = {This study investigates the ecological mechanisms governing the structure and composition of lung microbiome communities within tumor tissue from lung cancer patients. While this field has attracted increasing research attention, the ecological and etiological mechanisms driving microbial community assembly in this environment remain poorly characterized. To address this gap, we applied Sloan's near neutral model, Ning et al.'s normalized stochasticity ratio framework and Harris et al.'s multi-site neutral model to evaluate the influences of stochastic and deterministic factors at species, community and metacommunity levels, respectively. Our findings include: (i) Stochastic drift exhibited predominant influence at both species and community levels in normal adjacent tissue (NT), exceeding its effects in LUAD (lung adenocarcinoma) and LUSC (lung squamous cell carcinoma). (ii) At the metacommunity level, neutrality was not rejected at the metacommunity or local community levels, which is consistent with the previous finding (i). (iii) Elevated metacommunity biodiversity (θ) and immigration rates (m) in LUAD/LUSC compared to NT (observed in ∼50% of cases) suggest that tumor occurrence/progression may actively promote microbial recruitment to tumor microenvironments. We propose three non-exclusive mechanistic interpretations: (i) Tumor-mediated immune modulation creates permissive ecological niches; (ii) structural remodeling of tissue enhances microbial colonization potential; (iii) selective enrichment of opportunistic taxa (e.g., Streptococcus) through tumor-specific microenvironmental changes. Our results demonstrate that LUAD and LUSC microbiomes are shaped by deterministic tumor-driven selection, in contrast to the predominantly stochastic assembly observed in NT microbiomes. These findings reveal substantial reorganization of tumor-associated microbial communities, warranting further biomedical investigation and clinical validation.},
}

@article {pmid41207977,
year = {2025},
author = {Oliveira-Pinto, PR and Oliveira-Fernandes, J and Gramaje, D and Santos, C},
title = {Metabarcoding Profiling Reveals Microbiome Structure and Predicts Functional Shifts in Grapevines Challenged by Phyllosticta ampelicida.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {120},
pmid = {41207977},
issn = {1432-184X},
abstract = {Black rot disease (BRD), caused by the still understudied Phyllosticta ampelicida, is spreading across several grape producing countries, posing a growing threat to the agroindustry. The role of the grapevine microbiome in defending against this pathogen, particularly in terms of microbiota structure and community homeostasis, remains unclear. In this study, we aimed to characterize the epiphytic phyllosphere microbiota of grapevines and identify shifts in microbial genetic structure associated with BRD symptoms. We sampled three vineyards of the cultivar "Touriga Nacional" in the Douro region (Portugal), collecting 20 leaves from (a) five healthy and (b) five BRD-symptomatic grapevines. The presence of P. ampelicida was confirmed in all symptomatic samples. Epiphytic bacterial DNA was extracted and sequenced using next-generation sequencing (NGS). Results indicate that although overall the diversity and richness indexes were not different in diseased plants compared to healthy ones, there was a reduction in OTU richness in black rot-affected grapevines. Diseased plants exhibited significant shifts in microbial network assemblages and showed an increased relative abundance of certain taxa, such as Acinetobacter, suggesting a possible recruitment of beneficial bacteria in response to biotic stress. Additionally, we observed a higher abundance of antibiotic resistance-related KEGG Orthologues (KOS) in symptomatic plants, raising potential concerns for human health. This study presents the first characterization of the grapevine phyllosphere epiphytic bacterial microbiota and its structural shifts in response to BRD.},
}

@article {pmid41207775,
year = {2026},
author = {Belzer, A and Coates, SJ},
title = {Climate Change and Infectious Diseases in Dermatology.},
journal = {Dermatologic clinics},
volume = {44},
number = {1},
pages = {45-65},
doi = {10.1016/j.det.2025.08.003},
pmid = {41207775},
issn = {1558-0520},
abstract = {Human activities have led to climate change, resulting in global warming, ocean warming, and more frequent extreme weather events (EWEs). Each of these has the potential to amplify infectious diseases with skin manifestations. Alterations in the skin microbiome due to rising temperatures and humidity may increase infection risk. Global warming has led to expanding geographic ranges of vector-borne diseases. Warming waters have similarly increased the risk of waterborne diseases. EWEs are associated with increased incidence of cutaneous infections. Land-use change, both a cause and effect of climate change, increases the risk of zoonotic spillover.},
}

@article {pmid41207773,
year = {2026},
author = {Fernandez, K and Mundada, M and So, A and Wei, ML},
title = {Influence of Climate on Atopic Dermatitis.},
journal = {Dermatologic clinics},
volume = {44},
number = {1},
pages = {27-34},
doi = {10.1016/j.det.2025.08.007},
pmid = {41207773},
issn = {1558-0520},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease driven by immune dysregulation and skin barrier defects. This article summarizes the impact of climate change on AD outcomes, focusing on articles published since April 2023. Climate change amplifies environmental stressors, temperature extremes, altered humidity, and rising air pollution, that can trigger or worsen AD symptoms by increasing oxidative stress, disrupting the skin's microbiome, and weakening barrier function. Studies suggest associations between climate variables and AD outcomes, although findings are inconsistent. Strategies such as patient education, indoor air filtration, and broader policy measures to reduce pollution may mitigate climate-related risks.},
}

@article {pmid41207432,
year = {2025},
author = {Afonso, RB and Adivi, LN and Linehan, K and O'Donovan, M and Hill, C and Ross, RP and Stanton, C},
title = {Potential of silage inoculants to mitigate methane production from the rumen: A systematic review.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27063},
pmid = {41207432},
issn = {1525-3198},
abstract = {Methane (CH4) emissions from enteric fermentation in ruminants represent the largest source of anthropogenic agricultural emissions, contributing significantly to global CH4 levels. Enteric CH4 mitigation strategies have been intensively investigated to address the detrimental effects on climate change and ruminant production characteristics. This systematic review investigated whether microbial silage inoculants could reduce CH4 formation in the rumen microbiome, both ex vivo and in vivo, based on available literature. Two independent reviewers conducted a comprehensive search for peer-reviewed articles, without year restrictions, up to January 31, 2024. The search focused on studies reporting CH4 gas production both in vitro and in vivo. Of 434 articles initially identified, only 10 met the quality criteria and were included in the analysis. Among the selected studies, 9 measured CH4 production using in vitro assays, whereas one reported an in vivo trial. The majority of the experiments (70%) were conducted using cattle rumen samples, including the in vivo study involving cattle, the remainder of the experiments used rumen samples obtained from sheep. Ten bacterial species were used as inoculants across the selected studies. Lactobacillus buchneri, used in combination with additives, achieved the highest CH4 reduction at 83%. Lactobacillus plantarum also showed a significant reduction in CH4 output, achieving a 48% decrease. Overall, 80% of the reviewed studies reported a reduction in CH4 production by ruminant microorganisms following the application of silage microbial inoculants. These findings suggest that silage microbial inoculants hold promise as a strategy to mitigate CH4 emissions in livestock. The limited number of studies highlights the need for further research to confirm these results and explore wider applications.},
}

@article {pmid41207348,
year = {2025},
author = {Wang, X and Liu, P and Yang, L and Zheng, W and Zhu, L and Kong, X},
title = {Integrated analysis of trichlorfon-induced intestinal toxicity in Micropterus salmoides: Barrier Impairment, microbiome disruption, and metabolic reprogramming.},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {110988},
doi = {10.1016/j.fsi.2025.110988},
pmid = {41207348},
issn = {1095-9947},
abstract = {Trichlorfon is widely used to control parasites but may also induce sublethal effects in fish. However, its chronic effects on intestinal metabolism and toxicity remain unclear. Here, we investigated the effects of chronic trichlorfon exposure (0.01, 0.1, and 1 mg/L) on juvenile largemouth bass through integrated histological, physiological, microbiological, and metabolomic analyses. Trichlorfon exposure disrupted neurotransmitter balance, significantly reducing excitatory neurotransmitters (acetylcholine, glutamate, dopamine) and increasing gamma-aminobutyric acid. Mitochondrial dysfunction induced energetic stress and triggered a metabolic shift from oxidative phosphorylation to anaerobic glycolysis, supported by ATP depletion, accumulation of glycolytic and tricarboxylic acid intermediates, and downregulation of AMPKα1, PGC-1α, SDHa, and SDHb. Oxidative stress caused lipid peroxidation, decreasing linoleic and gamma-linolenic acids, and increasing malondialdehyde. Antioxidant defenses were suppressed, with impaired glutathione metabolism, decreased peroxidase and superoxide dismutase activities. Mucosal barrier was compromised, with disrupted glycosylation precursors, reduced expression of barrier genes (Occludin, ZO-1, Claudin-1), increased of proinflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α), and marked histopathological alterations. Altered polyunsaturated fatty acid metabolism promoted inflammatory eicosanoids (prostaglandin E2, 5(S), 14(R)-lipoxin B4). In addition, digestion and nutrient absorption were impaired, reflected by reduced conjugated bile acids, essential amino acids, and digestive enzyme activities. Gut microbial dysbiosis was observed, with increased opportunistic pathogens and reduced beneficial lactic acid bacteria. Overall, chronic trichlorfon exposure disrupted intestinal homeostasis. This study offers new insights into the intestinal metabolic alterations in fish exposed chronically to trichlorfon and highlights the need for prudent pesticide management in aquaculture.},
}

@article {pmid41207331,
year = {2025},
author = {Carlà, AS and Ianiro, G},
title = {Beneficial effects of physical exercise on anticancer immunity are mediated by gut microbiome metabolites.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.11.001},
pmid = {41207331},
issn = {1528-0012},
}

@article {pmid41207298,
year = {2025},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1152},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

@article {pmid41207233,
year = {2025},
author = {Basapuram, G and Duttagupta, S and Dutta, A},
title = {Pesticides impact microbial communities in the freshwater ecosystem: Implications on biogeochemical cycles.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140403},
doi = {10.1016/j.jhazmat.2025.140403},
pmid = {41207233},
issn = {1873-3336},
abstract = {Pesticides that discharge from surrounding environments into river water affect the composition and structure of the microbiome, eventually modifying the biogeochemical processes. Microcosm experiments examined the effects of two prevalent pesticides (malathion and atrazine) on the river water microbiome. 16S rRNA gene amplicon sequencing was leveraged to characterize microbiome shifts in the presence and absence of pesticides. Microbial diversity was significantly reduced in the presence of pesticides. The presence of malathion and atrazine in higher abundances promoted the growth of Pseudomonas while inhibiting the expansion of other microorganisms. Principal Coordinates Analysis indicated compelling differences in diversity and metabolic profiles. Shifts in microbial populations involved in carbon, nitrogen, and sulfur cycles were observed in the presence of pesticides. Our findings demonstrated a reduction in microbial populations involved in carbon fixation and sulfur oxidation in samples exposed to pesticides compared to samples unamended with pesticides. With respect to the nitrogen cycle, the microorganisms involved in nitrification and denitrification processes were reduced in the presence of pesticides. This study exemplifies an intricate interplay between pesticide application, microbial diversity, and the associated metabolic activities, which highlights the multifaceted impact of emerging contaminants that contribute to a cascading effect on the biogeochemical cycles.},
}

@article {pmid41207116,
year = {2025},
author = {Obayashi, N and Shintani, T and Morihara, N and Kawada-Matsuo, M and Ando, T and Miyata, R and Hayashi, Y and Kataoka, N and Tanimoto, K and Kawaguchi, H and Komatsuzawa, H and Kajiya, M},
title = {Prevalence and Ecological Role of Streptococcus toyakuensis in Saliva of Healthy Young Individuals.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {103987},
doi = {10.1016/j.identj.2025.103987},
pmid = {41207116},
issn = {1875-595X},
abstract = {BACKGROUND AND OBJECTIVES: Antimicrobial resistance (AMR) remains a critical global health concern. In 2022, Streptococcus toyakuensis, a newly identified species with potential multidrug resistance, was isolated from the blood of a patient with sepsis. This study aimed to explore the distribution of S. toyakuensis in the oral microbiome of healthy young individuals and to compare the bacterial community composition between the detection and non-detection groups.

METHODS: Sixty saliva samples were randomly collected from 356 healthy young individuals and analyzed using next-generation 16S rRNA sequencing for comprehensive microbial profiling. A taxonomic distribution analysis was performed to compare microbial diversity between S. toyakuensis detection and non-detection groups. Functional analysis identified differentially activated metabolic pathways.

RESULTS: S. toyakuensis was detected in 35 of 60 participants. Beta diversity analysis revealed a significant difference in microbial composition between the groups. Linear discriminant analysis effect size showed higher abundance of Neisseria, Haemophilus, Campylobacter, and Capnocytophaga in the detection group, while Actinomyces predominated in the non-detection group. Functional analysis identified 26 significantly different metabolic pathways, including the glyoxylate cycle and L-methionine biosynthesis superpathway.

CONCLUSION: The high prevalence of S. toyakuensis in the oral microbiome of healthy young individuals highlights the need for further investigation into its role in AMR dissemination.

CLINICAL SIGNIFICANCE: The colonization of S. toyakuensis may influence the oral microbial ecosystem and metabolic activity, potentially facilitating the spread of AMR. Its detection in healthy individuals suggests a silent reservoir, underscoring the importance of oral microbiome surveillance in public health and infection control strategies.},
}

@article {pmid41207099,
year = {2025},
author = {Torres, AHF and Soares, TA and Pereira, RB and Gomes, P and Garrido, SS},
title = {Interplay between the immune system and the microbiome of human skin and its modulation by antimicrobial peptides.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115754},
doi = {10.1016/j.intimp.2025.115754},
pmid = {41207099},
issn = {1878-1705},
abstract = {The cutaneous immune system is essential for protecting the body against pathogens and regulating the skin's immune response, which can be further influenced by the skin's microbiome and also by exogenous bioactive compounds. As such, innovative approaches based on use of antimicrobial peptides and/or probiotics show a promising potential for restoring skin homeostasis and alleviating dermatological conditions. In this connection, herein we revise the immune functions of the skin, covering its structural and cellular components, interactions with the microbiome, and defense mechanisms as well as their modulation by antimicrobial peptides. We further address recent developments in this topic, providing an up-to-date perspective that paves the way for advancing both skin immunology knowledge and new therapeutic interventions for a healthy skin.},
}

@article {pmid41207093,
year = {2025},
author = {Li, Y and Yu, R and Tan, S and Sun, L and Yan, Y and Huang, J and Waseem, MH and Wang, Z and Li, C},
title = {Alterations in the profiles of rumen microbiota and metabolites in Holstein and Jersey dairy cows under heat stress.},
journal = {Journal of thermal biology},
volume = {134},
number = {},
pages = {104327},
doi = {10.1016/j.jtherbio.2025.104327},
pmid = {41207093},
issn = {0306-4565},
abstract = {High temperature impacts the performance and health of dairy cows in summer, causing considerable financial burden in the dairy industry. Differences in physiological changes, rumen microbial diversity and metabolites of Holstein and Jersey dairy cows under heat stress and normal environment were investigated. The present study demonstrates that oxidative stress levels in Holstein and Jersey cows are significantly elevated under conditions of heat stress, while the pro-inflammatory cytokine levels were elevated only in heat-stressed Holstein cows. 16S rDNA gene sequencing showed that heat stress markedly altered the abundance, homogeneity and makeup in the bovine rumen microbiome. Moreover, the significant abundance of Rikenellaceae_RC9_gut_group exhibited a positive association with malondialdehyde (MDA) in Holstein cows, Pseudobutyrivibrio was positively correlated with tumor necrosis factor-α (TNF-α) in the Jersey cows. Metabolomics profiling based on liquid chromatography-mass spectrometry (LC-MS) revealed that totally 1065 metabolites in Holstein cows and 571 metabolites in Jersey cows were significantly changed. The differential metabolites Leucine and Prostaglandin i2 were negatively associated with interleukin (IL)-6, Erucamide was positively related to IL-1β and MDA in Holstein cows. And 9,10-dihydroxy-12z-octadecenoic acid showed a negative correlation with IL-6 and TNF-α in Jersey cows. Besides, the changed rumen microbiome displayed remarkable associations with metabolites. Our results indicated that heat stress caused remarkable alterations of rumen microbiome and metabolism both in Holstein and Jersey dairy cows, the altered ruminal bacteria and metabolic profiles could consecutively affect physiological responses in dairy cows.},
}

@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: Tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}

@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}

@article {pmid41206876,
year = {2025},
author = {Catano, CP and DuBose, JG and Fuller-Hall, L and Chavez, J and de Roode, JC},
title = {Experimental Immigration Mediates Ecological Selection and Drift in Monarch Microbiome Assembly.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70252},
doi = {10.1111/ele.70252},
pmid = {41206876},
issn = {1461-0248},
support = {IOS-2202255//National Science Foundation/ ; },
abstract = {The distribution of biodiversity depends on processes operating across scales, yet multiscale paradigms have struggled to permeate host-microbiome research. Instead, host-microbiome research has focused on host selection and has struggled to explain the high variation in microbial composition across individuals. By integrating multi-scale ecological theory with experimental manipulation of bacteria colonizing monarch butterfly caterpillars, we test the hypothesis that immigration from the regional species pool alters the importance of niche selection and drift in causing variation in gut bacterial communities across individuals and through ontogeny. Higher immigration increased the dominance of certain bacteria, causing greater convergence in bacterial composition across the caterpillar life stage. Conversely, limited immigration made colonization more stochastic, resulting in more unpredictable variability in bacterial composition across individuals. Our study reveals that immigration mediates the balance between host selection and drift, demonstrating that processes operating at scales beyond the individual are underappreciated but critical for structuring host-microbiome symbioses.},
}

@article {pmid41206864,
year = {2025},
author = {Docherty, JAD and Cook, R and Kiu, R and Dyball, X and Brown, TL and Kujawska, M and Smith, RL and Phillips, S and Watt, R and Telatin, A and Tiwari, SK and Hall, LJ and Adriaenssens, EM},
title = {Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary "arms race" dynamics.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116542},
doi = {10.1016/j.celrep.2025.116542},
pmid = {41206864},
issn = {2211-1247},
abstract = {Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, as drivers of gut bacterial composition, can affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore direct interactions between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. Analysis of 1,086 bifidobacterial genomes reveals the presence of complex systems that prevent viral invasion, with 34 defense systems and 56 subtypes detected, including several different CRISPR-Cas systems. CRISPR spacers target almost three-quarters of bifidobacteria-derived prophages, indicating dynamic interactions. At least one prophage is present in ∼67% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. These prophages encode various defense and anti-defense systems, such as anti-CRISPR genes and restriction-modification mechanisms. Overall, this investigation reveals that coevolutionary "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.},
}

@article {pmid41206708,
year = {2025},
author = {Royer, FP and Schlick-Steiner, JS and Klammsteiner, T and Kopf, T and Schlick-Steiner, BC and Steiner, FM},
title = {Bacterial communities of wild bee species and the western honey bee (Apis mellifera) (Hymenoptera: Apoidea): Alpine insights.},
journal = {Journal of insect science (Online)},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/jisesa/ieaf095},
pmid = {41206708},
issn = {1536-2442},
abstract = {Wild bees are decreasing in species diversity and populations due to human impact. The abundance of the western honey bee (Apis mellifera L.) experiences an inverse trend, enhancing competition with wild bees and the probability of microbiome exchange. Addressing this exchange, we studied the gut microbiome composition of wild and honey bees, focusing on patterns indicating honey bee influence. Three solitary wild bee species (large scabious mining bee [Andrena hattorfiana F.], grey-backed mining bee (Andrena vaga Panzer), and European orchard bee [Osmia cornuta Latreille]) as well as bumble bees as representatives of eusocial wild bees (Bombus spp. Latreille) and honey bees were sampled in the Austrian Alps. Subsequent 16S ribosomal DNA sequencing revealed the composition of the bacterial communities. The bee groups differed concerning their bacterial composition, with honey bees having the least variation among individuals and a low number of exclusive bacterial taxa and bumble bees the highest bacterial diversity. High honey bee densities corresponded with lower bacterial diversity in wild bees and a higher bacterial similarity between wild and honey bees. Some bacterial taxa were found for the first time in the studied bee groups. Furthermore, the composition of bacterial communities differed between solitary and social bees. We found the first hints that high honey bee density negatively impacts wild bees through alterations of wild bee microbiomes. Future studies should focus on understanding microbiome transmission mechanisms and their consequences for wild bees. Suggestions on how to consider wild bee fitness are indispensable in halting the biodiversity crisis.},
}

@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}

@article {pmid41206083,
year = {2025},
author = {Jain, SG and Vennam, SS and Dharmatti, G and Huey, SL and Kaur, P and Krishnan, S and Nandi, BK and Puri, S and Sesikaran, B and Srinivasan, S and Udipi, S and Voruganti, VS},
title = {Principles and Guidelines for the Practice of Precision Nutrition in the Indian Context: A Narrative Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf177},
pmid = {41206083},
issn = {1753-4887},
support = {//International Life Sciences Institute India (ILSI INDIA)/ ; },
abstract = {Precision and personalized nutrition represent a transformative shift in dietary recommendations, moving away from a one-size-fits-all approach to a more individualized strategy that considers genetics, epigenetics, the microbiota, and socio-cultural, environmental, and lifestyle factors. As the field of precision medicine evolves, clear principles and guidelines are essential for its application in clinical and public health settings. In this narrative review we aimed to provide the current principles and guidelines governing personalized nutrition to establish a comprehensive and standardized framework for effective application and development of personalized nutrition strategies. In this review we also emphasized the importance of involving regional and cultural perspectives while formulating nutritional plans with a particular focus on individuals with an Indian background. A comprehensive search of key databases spanning the past two decades identified several core principles of precision nutrition and their integration with sociocultural factors. The guidelines emphasize interdisciplinary approaches and technological advancements like AI and big data and also point toward the applicability and generalizability of these approaches across cultures and populations, specifically Indian. However, the integration of multiple data sources and the requirement for uniform protocols are major challenges. Notwithstanding these challenges, the field of individualized nutrition has great promise for the future of nutrition. Future research should focus on refining these guidelines and addressing existing gaps to enhance their efficacy and applicability in real-world settings.},
}

@article {pmid41206012,
year = {2025},
author = {Tan, EK and Wang, JDJ and Pettersson, S and Wang, Q and Takahashi, R and Poewe, W and Jankovic, J and Rascol, O},
title = {Faecal microbiota transplant for Parkinson's disease: promises and future directions.},
journal = {Brain : a journal of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/brain/awaf419},
pmid = {41206012},
issn = {1460-2156},
abstract = {There is considerable evidence linking alterations in gut microbiome composition with Parkinson's disease (PD), leading to several recent randomized controlled fecal microbiota transplantation (FMT) trials in PD patients targeting gut dysbiosis with the aim to modulate the gut-brain axis. Some FMT trials have observed motor and non-motor symptoms improvements in PD patients, possibly through microbiota linked enhanced short-chain fatty acid or other metabolite effects and reduced systemic inflammation. While the findings are exciting and can potentially open a new treatment paradigm, crital questions on donor selection, the optimal screening and selection of the donor microbiome, delivery routes and the timing and frequency of transplantation need to be addressed. We suggest that future FMT trials should incorporate blood, metabolites, urine and functional neuroimaging biological markers and control dietary, lifestyle comorbidities, medication intake and/or other potential variables, and to ensure optimal evaluation of interactions between the gut microbes and brain outcomes prospectively over a longer time frame.},
}

@article {pmid41205933,
year = {2025},
author = {Favaron, A and Sangfuang, N and McCoubrey, LE and Awad, A and Ghyselinck, J and Marzorati, M and Verstrepen, L and De Munck, J and De Medts, J and Basit, AW and Orlu, M},
title = {Assessing the effects of tofacitinib on the gut microbiome in inflammatory bowel disease.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107365},
doi = {10.1016/j.ejps.2025.107365},
pmid = {41205933},
issn = {1879-0720},
abstract = {Gut microbiota dysbiosis and impaired epithelial barrier function play a key role in inflammatory bowel disease (IBD). Tofacitinib citrate, a Janus kinase (JAK) inhibitor approved for IBD, modulates immune responses via the JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway, yet its effects on the gut microbiome remain unclear. Here, we employed the short-term colon model (ProDigest, BE) containing human microbiota from three Crohn's Disease donors to assess fermentative and metabolic activities and microbial composition following 48 h of tofacitinib treatment. A Caco-2/THP1 co-culture system was used to assess the impact of tofacitinib on epithelial immunomodulation and barrier integrity. Tofacitinib did not significantly affect microbiota composition and fermentative or metabolic activity. However, it consistently reduced pro-inflammatory chemokines motif chemokine ligand 10 (CXCL10) and monocyte chemoattractant protein-1 (MCP-1), and interleukin-6 (IL-6) in specific donors, indicating targeted immunomodulatory effects. These findings suggest that while tofacitinib may have a minimal impact on microbiota function, it may exert anti-inflammatory effects via microbiota-derived metabolites. The short-term colon model represents a robust platform for investigating microbiome-drug interactions relevant to IBD.},
}

@article {pmid41205808,
year = {2025},
author = {Cohen, S and Donovan, M and Gardner, D and Sambo, D and Karagoz, SB and Cinar, R and Goldman, D and Gardner, JD and Pacher, P and Paloczi, J},
title = {Selective Depletion of Gut Gram-Negative Bacteria Attenuates Alcohol-Binge-Induced Cardiovascular Dysfunction by Lowering Cardiac Anandamide Levels.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.10.010},
pmid = {41205808},
issn = {1525-2191},
abstract = {Binge drinking contributes to a rising number of emergency room visits in the United States. Our previous work demonstrated that an alcohol binge impairs cardiac performance and exerts complex hemodynamic effects through the activation of the endocannabinoid-mediated cannabinoid receptor 1 (CB1R) signaling pathway. Anandamide (AEA), an endogenous CB1R agonist, is synthesized in response to various stressors and tissue injury. However, the role of binge drinking in increasing myocardial AEA levels, which leads to CB1R-dependent cardiodepression, remains unclear. Here, we studied how endotoxins from intestinal Gram-negative bacteria affect myocardial AEA levels, which further induce CB1R-dependent cardiac dysfunction following acute alcohol intoxication. Using a murine model of a single alcohol binge (5 g/kg orally), we observed reduced mesenteric microcirculation concurrent with elevated circulating endotoxin levels. Selective depletion of gut Gram-negative bacteria by antibiotics partially ameliorated alcohol-induced gut barrier dysfunction, significantly lowered circulating endotoxins, coinciding with reduced cardiac AEA levels at 3 hours post-binge. These changes were paralleled with moderately improved cardiac performance, and vascular tone. Cardiac RNA levels of genes involved in AEA synthesis increased after alcohol binge, but not in antibiotic-pretreated mice. However, acute alcohol-induced cardiac AEA formation was unrelated to Toll-like receptor-4 signaling. These findings provide novel insights that highlight the pivotal role of intestinal Gram-negative bacteria in modulating cardiac AEA levels after an alcohol binge, leading to cardiovascular dysfunction.},
}

@article {pmid41205786,
year = {2025},
author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Fritz, B and Bjarnsholt, T and Trivedi, U and Li, X and Sørensen, SJ and Herly, M},
title = {Breast Implant microbiome profile correlates with foreign body response severity.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.11.008},
pmid = {41205786},
issn = {1878-7568},
abstract = {Biomedical implants significantly enhance quality of life for millions of individuals worldwide. However, maintaining long-term implant function remains challenging, and it is often due to a severe foreign body response, characterized by fibrosis and functional impairment, clinically referred to as capsular contracture for breast implants. Colonization of implant surfaces by low-virulent bacteria has been proposed as a potential driver of severe foreign body response, but evidence from large-scale human studies has been lacking. We found that the implant microbiome composition is significantly associated with the foreign body response severity based on an extensive characterization of the breast implant microbiome using 16S rRNA gene amplicon sequencing. We analyzed 339 explanted breast implants from 206 patients undergoing revisional surgery without any symptoms of a clinical infection. We detected a diverse community of bacteria on the implants and demonstrated that an increased relative abundance of Staphylococcus was associated with a severe foreign body response. This pattern was supported by a within-patient analysis of 20 individuals with unilateral severe versus contralateral mild foreign body response. These findings suggest that the implant microbiome plays a role in the development of a severe foreign body response and may guide strategies to improve implant biocompatibility. STATEMENT OF SIGNIFICANCE: : This study identified a diverse microbiome on breast implants from patients without any symptoms of infection and demonstrated a clear association between microbiome composition and the severity of the foreign body response (FBR), a significant complication affecting implant function. Notably, implants with severe FBR showed lower microbial diversity and higher relative abundance of Staphylococcus compared to those with mild FBR. Additionally, a paired analysis within patients with severe FBR in one breast and mild FBR in the contralateral breast further supported higher relative Staphylococcus abundance on the severe FBR implant. These findings provide insights into microbial factors influencing implant biocompatibility, which may guide strategies to improve implant biocompatibility and reduce complications for patients.},
}

@article {pmid41205726,
year = {2025},
author = {Tao, H and Mao, K and Zhang, Z and Wei, W and Huang, X and Chen, Y and Mei, S and Tian, X},
title = {Applications of traditional Chinese medicine in cancer immunotherapy via gut microbiota modulation: Current status, mechanisms, challenges and perspectives.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108020},
doi = {10.1016/j.phrs.2025.108020},
pmid = {41205726},
issn = {1096-1186},
abstract = {Cancer immunotherapy faces significant limitations due to therapeutic resistance. Emerging evidences have identified the gut microbiota (GM) as a crucial regulator of antitumor immunity through its effects on the tumor immune microenvironment (TIME). Guided by the principle of "fu zheng qu xie" (fortifying healthy qi to reinforce immune homeostasis and eliminating pathogenic factors to promote immune clearance), traditional Chinese medicine (TCM) exerts multi-target systemic regulation. Specifically, TCM modulates gut microecology, which in turn regulates the production of microbial metabolites (e.g., short-chain fatty acids, bile acids), ultimately reprogramming TIME by enhancing immune cell infiltration into the tumor parenchyma, optimizing T-cell cytotoxicity and differentiation, improving antigen presentation, and alleviating immunosuppression. This review systematically summarizes the causal chain of "TCMGMmetabolitesimmune cellsTIME" across different immune phenotypes, emphasizing how bioactive TCM components and classical formulas reshape microbial communities, enrich beneficial bacteria, and regulate metabolic pathways to potentiate cancer immunotherapy. Despite promising preclinical data, challenges persist due to mechanistic complexity, the lack of standardization, and limited clinical translation. Potential solutions include multi-omics integration, intelligent screening of herbal compounds, and targeted delivery systems. With advancing pharmacological insights, TCM-derived microbiome modulators (TMMs), defined as phytochemicals and formulations that systematically modulate gut microecology, may overcome immunotherapy resistance, representing a novel strategy for enhancing cancer immunotherapy.},
}

@article {pmid41205590,
year = {2025},
author = {Golob, JL and Oskotsky, TT and Tang, AS and Roldan, A and Chung, V and Ha, CWY and Wong, RJ and Flynn, KJ and Chai, R and Dubin, C and Parraga-Leo, A and Wibrand, C and Minot, SS and Oskotsky, B and Andreoletti, G and Kosti, I and Bletz, J and Nelson, A and Gao, J and Wei, Z and Chen, G and Tang, ZZ and Novielli, P and Romano, D and Pantaleo, E and Amoroso, N and Monaco, A and Vacca, M and De Angelis, M and Bellotti, R and Tangaro, S and Wang, Z and Yao, J and Goel, A and Mao, J and Wang, H and Zhang, Y and Tewari, A and Kuntzleman, A and Bigcraft, I and Techtmann, S and Bae, D and Kim, E and Jeon, J and Joe, S and , and Theis, KR and Ng, S and Lee, YS and Diaz-Gimeno, P and Bennett, PR and MacIntyre, DA and Stolovitzky, G and Lynch, SV and Albrecht, J and Gomez-Lopez, N and Romero, R and Stevenson, DK and Aghaeepour, N and Tarca, AL and Costello, JC and Sirota, M},
title = {Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102428},
doi = {10.1016/j.xcrm.2025.102428},
pmid = {41205590},
issn = {2666-3791},
}

@article {pmid41205569,
year = {2025},
author = {Mayr, AV and Weinhold, A and Nolzen, A and Keller, A and Ayasse, M},
title = {The neonicotinoid Acetamiprid alters the chemical profile of the primitive eusocial bee Lasioglossum malachurum.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119311},
doi = {10.1016/j.ecoenv.2025.119311},
pmid = {41205569},
issn = {1090-2414},
abstract = {The widespread use of agrochemicals, particularly neonicotinoids, poses a significant threat to the health of (pollinating) insects. Various health traits are affected, but the impact on the chemical communication of wild bees remains a poorly studied aspect. Here, we assessed how field-realistic exposure to the 'honeybee-safe' neonicotinoid Acetamiprid affects the behaviour, cuticular lipids and microbiome of Lasioglossum malachurum, a small ground-nesting sweat bee. L. malachurum is an important, abundant pollinator of several crop plants with primitive social behaviour which relies on cuticular lipids for communication. We collected bees in the field for a controlled pesticide treatment in the lab. Pesticide-treated individuals increased their sugar-water consumption rate compared to the control group. After 7 days of experiment, the treatment group showed a trend towards less developed ovaries and an increased amount of odour with significantly altered queen pheromones. While the microbiome was not affected by the treatment, a comparison with field individuals showed an erosion of their gut microbiome with a reduction in Apilactobacillus during laboratory keeping. Our findings indicate that neonicotinoids may disturb chemical communication in L. malachurum and thus might impair social behaviour. This raises concerns about the threats of currently approved pesticides to wild pollinators.},
}

@article {pmid41205563,
year = {2025},
author = {Bautzmann, R and Waelchli, J and Schürch, S and Schlaeppi, K and Rentsch, D},
title = {Biodegradable plastics impair maize growth and reshape bacterial communities associated with roots and sand or soil.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119353},
doi = {10.1016/j.ecoenv.2025.119353},
pmid = {41205563},
issn = {1090-2414},
abstract = {Biodegradable plastics entering terrestrial ecosystems raise environmental and food safety concerns, as they impact soil-plant systems either directly by releasing compounds during degradation, or indirectly, by altering soil biophysical properties and/or microbial communities. Here, we examined the impact of biodegradable micro- and macroplastics made from Mater-Bi, and starch (a simple carbon [C] source present in the plastic studied) on the growth of Zea mays seedlings and bacterial communities associated with roots or with the growth substrates, i.e., sand or silt loam soil. Increasing concentrations of biodegradable plastics and starch reduced plant biomass and chlorophyll content in a dose-dependent manner. Additionally, nitrogen (N) content was reduced, accompanied by lower transcript levels of genes commonly downregulated under N-limiting conditions. Biodegradable plastics and starch altered the bacterial community composition, resulting in decreased bacterial diversity in the growth substrates and increased diversity within maize roots. The effects on maize and bacteria were consistent but generally stronger in sand than in silt loam soil. A follow-up experiment confirmed that plastics- or starch-associated microbes did not affect maize growth when no plastics or starch was present. Our results suggest that biodegradable plastics significantly impair soil-plant systems through their C inputs.},
}

@article {pmid41205502,
year = {2025},
author = {Song, HW and An, J and Sha, JQ and Hu, FY and Liu, WT},
title = {Ca(II) alleviates microplastic toxicity to Microcystis aeruginosa via cyanobacteria induced carbonate precipitation.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140341},
doi = {10.1016/j.jhazmat.2025.140341},
pmid = {41205502},
issn = {1873-3336},
abstract = {Microplastics (MPs), as a globally emerging contaminant, present significant and increasing threats to aquatic ecosystem health and adversely impact cyanobacterial physiology. Ca(II) are ubiquitous essential ions in natural waters, yet their influence on MPs toxicity to cyanobacteria remains insufficiently understood. This study systematically investigated the mitigating effects and mechanisms of Ca(II) on MPs-induced toxicity in Microcystis aeruginosa through an integrated approach involving toxicological assays, microscopic characterization, and microbiome analysis. Both low (2 mg L[-1]) and high (10 mg L[-1]) concentrations of MPs induce oxidative stress and inhibit the growth of M. aeruginosa. However, the addition of Ca(II) significantly mitigated these adverse effects. Mechanistically, Ca(II) promoted cyanobacteria induced carbonate precipitation (CICP), leading to the immobilization of approximately 32.3-34.7 % of MPs, thereby reducing cellular exposure to MPs. Consequently, this attenuated MPs-induced stress on glucosiolate biosynthesis and 2-oxocarboxylic acid metabolism pathways, while mitigating damage to photosynthetic components, including photosystem II (PSII), photosystem I (PSI), and the photosynthetic electron transport chain (PETC). This study provides evidence that Ca(II) protects M. aeruginosa from MPs toxicity by activating the CICP pathway to establish a calcite-based defense system. These findings enhance our understanding of cyanobacteria-MPs interactions under environmentally relevant ionic conditions.},
}

@article {pmid41205302,
year = {2025},
author = {Camille, E and Sébastien, B and Virginie, B},
title = {The hidden players: The mycobiome of pancreatic ductal adenocarcinoma tumors.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128392},
doi = {10.1016/j.micres.2025.128392},
pmid = {41205302},
issn = {1618-0623},
abstract = {The microorganisms that inhabit the human body are known to play a role in human health and disease. Continuing to elucidate their specific role in disease progression is, however, necessary. The imbalance of these microorganisms-known as dysbiosis-has been linked to a myriad of intestinal diseases, and more recently to cancer. Despite making up less than 0.1 % of the human microbiome, dysbiosis of the fungal component of the microbiome-the mycobiome-has been found to contribute to the tumorigenesis and progression of certain types of tumors, pancreatic ductal adenocarcinoma (PDAC) included. The quantity and composition of the mycobiome was found to differ between healthy pancreatic tissue, the gut mycobiome of PDAC patients and PDAC tissue. Moreover, in a murine model of PDAC, it was shown that fungal ablation had a protective effect on tumor growth, and that specific fungal species, such as Malassezia globosa, contribute to tumor growth as well as to the inflammatory environment observed in PDAC tumors which promotes tumor progression. Research shows that fungal presence contributes to shaping the immune microenvironment through the activation of the complement system and/or by eliciting a type 2 immune response. Despite these preliminary findings, given the novelty of the field and of the bioinformatics pipelines used to analyze sequencing data, standardized approaches are still under development, thus leading to disagreement on the reliability of these results. The purpose of this review is to provide an up-to-date overview of the current research regarding the contribution of the fungal mycobiome in PDAC tumor progression and the overall tumor microenvironment (TME) of PDAC tumors.},
}

@article {pmid41205272,
year = {2025},
author = {Ai, Y and Davis, AB and Basta, NT and Lee, J},
title = {Unveiling profiles: Dredged materials from Lake Erie harbors are reservoirs for toxic cyanobacteria, antimicrobial resistance, and nutrients.},
journal = {The Science of the total environment},
volume = {1005},
number = {},
pages = {180879},
doi = {10.1016/j.scitotenv.2025.180879},
pmid = {41205272},
issn = {1879-1026},
abstract = {The beneficial use of dredged materials (DMs) as an agricultural resource has gained popularity. Lake Erie shorelines are the most dredged of the Great Lakes in the United States, which is also affected by anthropogenic-driven harmful algal blooms (HAB) and other pollutants like antibiotic resistance genes (ARGs). This study focused on characterizing the DMs from six harbors along the southwest shore of Lake Erie, focusing on the toxic cyanobacteria, toxins, nutrients, microbiome, resistome, and their bacterial hosts. Dominated toxic cyanobacteria genera in DMs are Microcystis, Dolichospermum, Nostoc, Aphanizomenon, and Planktothrix. with microcystin (MC)-producing Microcystis being the major toxin producer. In line with the spatial bloom distribution in Lake Erie, from the central to western basin, the concentration of MC and toxic cyanobacteria in DMs increased. The same spatial trend was observed regarding the ARG, nitrogen, and phosphorus concentrations in DMs. The concentration of clinically relevant ARGs (blaKPC, blaNDM, blaOXA-48, tetQ, and sul1) was positively correlated with the toxic cyanobacteria, N, and P concentrations. Overall, this study provides valuable information on DMs from cyanobacteria- and AR-affected eutrophicated lakes, so safe DM management plan and dredging operations can be possible to sustain beneficial use of DMs in the HAB-affected areas.},
}

@article {pmid41205133,
year = {2025},
author = {Ghafoor, DD and Ahmad, DO and Najmuldeen, HH and Mohammed, SJ and Jalal, PJ and Mustafa, FS and Alghofaili, F and Zangana, BA and Al-Bajalan, SJ},
title = {Multiple sclerosis pathophysiology: a comprehensive review of genetic, environmental, and immunological drivers.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41205133},
issn = {1568-5608},
abstract = {Multiple sclerosis (MS) is a complex, chronic neuroinflammatory and neurodegenerative disorder of the central nervous system. This comprehensive review synthesizes evidence to argue that the paramount challenge in MS is bridging the disconnect between anti-inflammatory therapies and ineffective neuroprotective strategies, necessitating a dual-target approach. The paper discusses the crucial roles of genetic predisposition, highlighting the HLA-DRB1*15:01 allele and other non-HLA loci, and environmental triggers, such as Epstein-Barr virus infection, vitamin D deficiency, and smoking. We detail the dysregulation of both T-cells (Th1 and Th17 subsets) and B-cells in the autoimmune attack on myelin, as well as the intricate mechanisms of neurodegeneration, axonal damage, and the challenges of remyelination. The review also incorporates emerging insights into the role of the gut microbiome and epigenetic modifications, underscoring the necessity of an integrative model to understand MS pathogenesis. Ultimately, this review provides a foundational understanding of converging biological drivers of MS. Therapeutically, currently approved disease-modifying therapies (DMTs)-including interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, and anti-CD20 monoclonals-reduce relapse frequency and MRI activity but do not eliminate disability progression, particularly in progressive MS. Acute relapses are treated with high-dose corticosteroids, with plasma exchange reserved for steroid-refractory cases. We therefore argue that future success requires integrated strategies that couple sustained control of peripheral inflammation with CNS-intrinsic neuroprotection and remyelination. Therapeutically, modern disease-modifying therapies (interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, anti-CD20 monoclonals including ocrelizumab, ofatumumab, and ublituximab) reduce relapse rates and MRI activity yet do not consistently prevent disability progression-particularly in non-active progressive MS. Acute relapses are treated with high-dose corticosteroids; plasma exchange is reserved for steroid-refractory attacks. These realities motivate mechanism-informed strategies that pair sustained immune control with CNS-intrinsic neuroprotection and remyelination.},
}

@article {pmid41205097,
year = {2025},
author = {Lee, SJ and Lee, YS and Kim, YR and Jeon, MH and Noh, DI and Jeong, SM and Kim, KW and Lee, EW and Jang, WJ},
title = {Development of Novel Host-Associated Low-Temperature Probiotics (HALP) Tailored to Aquaculture Applications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41205097},
issn = {1867-1314},
support = {R2025038//National Institute of Fisheries Science/ ; 2022R1A2C1012655//National Research Foundation of Korea/ ; RS-2024-00403688//Korea Basic Science Institute/ ; },
abstract = {Aquaculture temperatures vary depending on the fish species, and probiotics used in aquaculture must remain effective under these conditions. Therefore, our study developed host-associated low-temperature probiotics (HALP) adapted to temperature conditions relevant to aquaculture. Three bacterial strains, Rahnella inusitata NBL2302 (RI), Pseudoalteromonas arctica NBL2303 (PA), and Lactiplantibacillus plantarum NBL2306 (LP), were isolated from the gastrointestinal tract of Korean rockfish (Sebastes schlegelii). Safety assessments, in vitro probiotic characterization (including antioxidant activity, acid/salt/bile tolerance, antimicrobial activity, and adhesion), and a feeding trial were conducted. All three strains were confirmed to be safe, exhibiting no hemolytic or cytotoxic activity. Among the three strains, LP exhibited the highest adhesion to intestinal epithelial cells and showed antimicrobial activity against fish pathogens. RI supplementation significantly enhanced innate immune markers such as serum total protein (TP), triglycerides (TG), and myeloperoxidase (MPO), along with the upregulation of immune-related genes (HSP70, IL-1β, TNF-α) (p < 0.05). PA supplementation resulted in the greatest weight gain and significantly improved specific growth rate (SGR), likely due to increased digestive enzyme activity. LP promoted immunostimulatory responses (elevated expression of MPO, TP, HSP70, and TNF-α) and pronounced changes in the beta diversity of the gut microbiota. Microbiome analysis revealed that LP-fed fish harbored higher abundances of beneficial genera such as Pseudomonas, Ralstonia, and Sphingomonas. Overall, each strain displayed unique characteristics and exerted distinct effects during feeding trials. These findings, which take host temperature preferences into account, underscore the potential of HALP in aquaculture and highlight the need for further research into optimized combination strategies.},
}

@article {pmid41204383,
year = {2025},
author = {Issifu, S and Elango, AV and Michl, K and David, C and Cernava, T and Wilhelm, RC and Rasche, F},
title = {Perennial Kernza cropping promotes rhizosphere microbiome stability and endophyte recruitment compared to annual wheat.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {139},
pmid = {41204383},
issn = {2524-6372},
support = {RA 1717/8-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Perennial cropping systems are increasingly recognized for their potential to enhance microbial biodiversity and beneficial soil functions compared to annual crops. The impact of perennialization on the rhizomicrobiome and endophyte community was assessed by comparing intermediate wheatgrass (Thinopyrum intermedium, commercialized as Kernza®, hereafter called 'Kernza') and annual wheat (Triticum aestivum) associated communities across a north-south European agroclimatic gradient (Sweden, Belgium, and France) over two growing seasons and at two depths.

RESULTS: Between the 2 years, the Kernza-associated rhizomicrobiome was more stable and exhibited greater homogeneity across depths compared to annual wheat. Kernza harboured a significantly more diverse set of crop-associated amplicon sequence variants (ASVs) and had a higher number of core ASVs than annual wheat. Furthermore, Kernza had a significantly higher proportion of rhizobacterial populations in root tissues than annual wheat. Environment-wide association analyses revealed that the Kernza rhizosphere had higher proportions of grassland-associated and rhizosphere-dwelling microbiomes compared to annual wheat. Despite these noteworthy differences, the greatest variation in the rhizomicrobiome composition was driven by factors such as country, year, and depth, rather than crop type. For instance, Actinobacteriota dominated rhizobacterial communities in both Kernza and annual wheat.

CONCLUSIONS: Overall, Kernza conferred modest yet clear improvements in rhizomicrobiome community stability and selective endophyte recruitment, supporting its ability to enhance sustainable, microbially-mediated soil functions. Moreover, Kernza hosted significant grassland-associated taxa, suggesting a similarity between Kernza fields and grassland ecosystems.},
}

@article {pmid41204381,
year = {2025},
author = {Villette, R and Sunyer, JO and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Correction: Integrated multi‑omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {230},
pmid = {41204381},
issn = {2049-2618},
}

@article {pmid41204312,
year = {2025},
author = {Sun, W and Liu, Q and Chen, H and Xie, X and Zhang, Z and Zeng, Y and Zhou, J and Zhou, X and Jiang, X and Liang, Z and Li, JF and Deng, Y},
title = {Rice phyllospheric Pantoea spp. suppress blast and bacterial blight diseases.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {137},
pmid = {41204312},
issn = {2524-6372},
support = {2022YFA1304402; 2023YFD1400200//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Rice is a major food crop in China as well as Asia, yet its production is threatened by microbial diseases including blast disease caused by fungal pathogen (Magnaporthe oryzae) and bacterial blight caused by several bacterial pathogens. To screen for bacterial microbiota associated with rice blast occurrence, and/or contributing to disease resistance, we performed microbiota analysis with rhizosphere soil, root, stem, and leaf samples of blast susceptible (CO39) and resistant (Y33R) rice grown in a blast disease nursery garden.

RESULTS: Our result showed no significant difference in microbiota of rhizosphere soil, root, or leaf between these two rice cultivars, but stem microbiota were significantly different. Pantoea spp. were enriched in stem of blast susceptible rice, suggesting that it may play a role after fungal infection. A total of 822 bacterial strains were isolated from the phyllospheric (including leaf and stem) samples of Y33R and CO39 rice. Based on 16S rRNA amplicon sequencing, and phylogenic analysis using 16S rRNA, gyrB, leuS, and rpoB gene sequences, the 3 isolated strains and 1 strain were identified as P. ananatis and P. dispersa, respectively. The strains A25-H1 and B10-A1 were selected for genome sequencing, and based on Average Nucleotide Identity (ANI) analysis, we confirmed that A25-H1 was P. ananatis and B10-A1 was P. dispersa. The P. ananatis consortium (A25-F1, A25-G1, and A25-H1 combination) A25-11 and P. dispersa strain B10-A1 displayed suppressive effect on blast disease when they were applied to the susceptible rice CO39. Although a P. ananatis strain SC7 has been reported to cause bacterial blight in rice, A25-11 or B10-A1 was non-pathogenic to rice under experimental conditions. Furthermore, they could also suppress bacterial blight caused by SC7 or Xanthomonas oryzae pv. oryzae strain Pxo99A. A25-11 and B10-A1 did not affect the growth of M. oryzae mycelia in confrontation culture analysis, but induced transcription of rice immunity genes and promoted ROS accumulation, suggesting that the biocontrol effect of A25-11 or B10-A1 may lie on immunity priming. We further showed that A25-11 and B10-A1 possessed growth promoting capacity including indole 3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and siderophore production. Under field condition, the consortium A25-11 and strain B10-A1 could effectively suppress leaf and panicle blast.

CONCLUSIONS: Overall, this study established a microbiome method for identifying the rice bacterial communities of agricultural significance, with capacity of rice disease management and/or growth promotion.},
}

@article {pmid41204050,
year = {2025},
author = {Li, J and Wang, S and Luo, P and Li, Z and Gopinath, D},
title = {Exploring the plausible genetic relationship of salivary and tongue microbiome with periodontitis: A mendelian randomization study.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {76},
pmid = {41204050},
issn = {1013-9052},
abstract = {Chronic periodontitis (CP) is associated with subgingival microbial dysbiosis and demonstrates specific microbial patterns, though definitive causal connections with microbiomes in distinct anatomical regions remain undetermined. Genome-wide association datasets for CP and oral microbial communities were sourced from a large European cohort and China National GeneBank DataBase (CNGBdb), respectively. Employing single-nucleotide polymorphisms (SNPs) as genetic instruments, Mendelian randomization (MR) analyses were conducted through the inverse-variance weighted (IVW) approach. Analysis methods were implemented through the 'TwoSampleMR' package (v0.6.4) in R software. Sensitivity analyses were performed to validate the robustness of the findings and mitigate the occurrence of horizontal pleiotropy. The MR analyses revealed three salivary bacterial taxa, Neisseria meningitidis (OR = 0.67, 95% CI, 0.49-0.98), Streptococcus vestibularis (OR = 0.74, 95% CI, 0.56-0.98), and Lancefieldella unclassified (OR = 0.68, 95% CI, 0.52-0.91) to be significantly associated with a reduced risk of CP (p < 0.05). In contrast, tongue microbial taxa Solobacterium unclassified (OR = 1.45, 95% CI, 1.04-2.04), Fusobacterium sp000235465 (OR = 1.40, 95% CI, 1.02-1.94), and Haemophilus parainfluenzae (OR = 1.56, 95% CI, 1.12-2.18) were associated with an increased CP risk (p < 0.05). No evidence of heterogeneity and directional pleiotropy was noted for these associations. This study highlights the association between specific salivary and tongue microbial taxa and CP, providing mechanistic linkages into the plausible relationship. It also suggests that some microbial taxa may be further explored as indicators for risk-stratified preventive measures and novel targets for precision prebiotics and therapies.},
}

@article {pmid41204024,
year = {2025},
author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE},
title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {118},
pmid = {41204024},
issn = {1432-184X},
support = {GUN: CSUR23030681021//National Research Foundation/ ; },
mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.},
}

Animals
South Africa
*Bacteria/classification/genetics/isolation & purification
Goats/parasitology/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Sheep/parasitology
*Amblyomma/microbiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Goat Diseases/parasitology/microbiology/epidemiology
Phylogeny
*Sheep Diseases/parasitology/microbiology/epidemiology
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing

@article {pmid41203821,
year = {2025},
author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS},
title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39055},
pmid = {41203821},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; },
abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.},
}

Animals
Cattle
*Tight Junction Proteins/metabolism/genetics
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Rumen/microbiology/metabolism
Male
Tight Junctions/metabolism
Bacteria/genetics/classification

@article {pmid41203749,
year = {2025},
author = {Bowman, JP},
title = {Extensive fecal cast production and growth of Vibrionaceae in heat-stressed Atlantic salmon post-smolts.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39064},
pmid = {41203749},
issn = {2045-2322},
mesh = {Animals ; *Salmo salar/microbiology/physiology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Vibrionaceae/growth & development/genetics/isolation & purification ; *Heat-Shock Response ; RNA, Ribosomal, 16S/genetics ; Hot Temperature ; Female ; },
abstract = {Atlantic salmon (Salmo salar) are known to reduce or cease voluntary feeding and show altered digesta consistency under heat stress. This study was performed to determine what bacterial species occur and to characterize bacterial taxa and quantify changes in gut microbial abundance under heat stress. Atlantic salmon (all female, 1.5 kg average weight) in seawater tanks at 15 °C were fed for 2 to 4 weeks. Tank temperatures were increased to a 19 °C "warm phase" until voluntary feeding abated at which point tank temperatures were cooled to 15 °C for 4 weeks. At the end of each temperature phase the fish were stripped of feces and microbiome profiles were determined using 16 S rRNA V1-V3 metabarcoding. The tank experiment was repeated three times in successive years. Abundances of bacteria were determined using qPCR. Vibrionaceae comprised most reads after the warm phase completed. The prominent levels of Vibrionaceae were accompanied by a large predominance of cast (sloughed intestinal mucosa) containing fecal samples. Quantitative PCR (qPCR) estimated fecal Vibrionaceae cell populations increased 1.9-3.4 log units/g after the warm phase. This population then decreased by 0.3-1.1 log units/g by the end of the 15 °C recovery phase. The gut Vibrionaceae and non-Vibrionaceae compositions in the separate trials were different each time. The results indicated heat stress induced inappetence corresponds to increased cast production accompanied by predominance of Vibrionaceae. The predominance of different bacteria in each trial could be partly due to the different initial abundances of taxa in the inputted smolt. Vibrionaceae colonizing the Atlantic salmon gut should be the focus of studies on the microbiology of thermally induced inappetence and dysbiosis in Atlantic salmon.},
}

Animals
*Salmo salar/microbiology/physiology
*Feces/microbiology
Gastrointestinal Microbiome
*Vibrionaceae/growth & development/genetics/isolation & purification
*Heat-Shock Response
RNA, Ribosomal, 16S/genetics
Hot Temperature
Female

@article {pmid41203701,
year = {2025},
author = {Lee, Y and Seo, J and Di Camillo, B},
title = {SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39059},
pmid = {41203701},
issn = {2045-2322},
support = {IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; DI_C_BIRD2020_01//Department of Information Engineering of the University of Padova/ ; },
mesh = {*Gastrointestinal Microbiome ; *Machine Learning ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Biomarkers ; },
abstract = {Machine learning has been increasingly applied to microbiome data for biomarker discovery. However, microbiome datasets are typically high-dimensional, sparse, and correlated, which makes model training challenging and prone to overfitting. Previous studies have also reported that microbiome features exhibit binary-like characteristics, and that binarization does not necessarily reduce predictive performance. This observation motivated our work. Building on this idea, we propose a SHAP-based binarization pipeline. We first trained several machine learning models on raw continuous data and selected the best-performing model (random forest). Using SHAP values derived from the training set, we determined feature-specific thresholds that best separated positive and negative contributions. The dataset was then binarized using these thresholds and new models were trained on the transformed data. We evaluated this approach on gut microbiome abundance data (283 species, 220 genera, 1,569 individuals) to classify inflammatory bowel disease (IBD) versus healthy controls. The SHAP-based binarization consistently improved classification performance and interpretability compared with both continuous data and zero-threshold binarization. The best model's Matthews correlation coefficient increased from 0.884 to 0.928, with the largest improvements observed in non-tree-based models such as logistic regression and neural networks. SHAP summary plots also revealed clearer feature patterns, and biomarker rankings were more stable. In addition, the pipeline enabled us to identify a concise set of 17 microbial biomarkers associated with IBD. This study introduces a novel approach for microbiome data analysis by explicitly linking binarization thresholds to SHAP-derived feature contributions. Our approach was grounded in the observation of binary-like patterns revealed through SHAP values. Furthermore, although binarization inevitably raises concerns about information loss, our evaluation confirmed improvements not only in predictive performance but also in interpretability and biomarker stability, providing a broader validation of robustness. These findings highlight SHAP-based binarization as an effective strategy for high-dimensional microbiome data, with broad applicability and opportunities for future extension.},
}

*Gastrointestinal Microbiome
*Machine Learning
Humans
*Inflammatory Bowel Diseases/microbiology
Biomarkers

@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}

Humans
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Intensive Care Units, Neonatal
Metagenomics
Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Gestational Age
Enteral Nutrition

@article {pmid41203487,
year = {2025},
author = {Good, DA and Renwick, S and Caballero-Arias, H and O'Doherty, KC and Paulino, LC and Allen-Vercoe, E},
title = {Toward a Yanomami framework for ethical microbiome research.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.011},
pmid = {41203487},
issn = {1878-4380},
abstract = {This paper proposes an ethical framework for microbiome research with the Yanomami, an Indigenous Amazonian people, grounded in collaboration, reciprocity, and relational accountability. Key elements include dedicated funding for community-identified initiatives, sustained community-led ethical oversight, and meaningful benefit-sharing. This approach fosters trust and supports equitable, culturally aligned, and sustainable research collaboration.},
}

@article {pmid41203044,
year = {2025},
author = {Jagwani, S and Musumeci, L and Flores, L and Mackenzie, GG and Amiji, MM},
title = {Strategic modulation of the gastrointestinal microbiome to enhance pancreatic cancer immunotherapy.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104528},
doi = {10.1016/j.drudis.2025.104528},
pmid = {41203044},
issn = {1878-5832},
abstract = {Pancreatic cancer (PC) remains one of the most lethal malignancies, characterized by aggressive progression, late detection, and limited response to current therapies. Recent research has revealed that the gastrointestinal and intratumoral microbiomes are key modulators of immune regulation, metabolism, and epigenetic pathways, influencing tumor progression and therapeutic efficacy. This review summarizes the complex microbiome-PC interplay, emphasizing microbial modulation of inflammation, immunity, and treatment resistance. We also highlight microbiome-targeted strategies, such as probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, along with advanced drug-delivery platforms - including nanoparticles, engineered bacteria, and stimuli-responsive systems - for precise microbiome modulation. Integrating microbiome science with immunotherapy, nanotechnology, and epigenetic reprogramming offers promising opportunities to improve outcomes in PC.},
}

@article {pmid41203008,
year = {2025},
author = {Wang, Y and Hernandez, E and Junejo, MH and Damsky, W},
title = {Granuloma Annulare Patients Treated with JAK Inhibitors Show Cutibacterium acnes Expansion: A clue to the Mechanism Underlying Acneiform Eruptions Seen with JAK Inhibitors.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.10.600},
pmid = {41203008},
issn = {1523-1747},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202947,
year = {2025},
author = {Olsen, T and Elshorbagy, A and Johnson, JE and Nichenametla, SN and Dong, Z and Sambamurti, K and Richie, JP and Vinknes, KJ},
title = {Sulfur amino acids, metabolic health and beyond: Recent advances, translational implications, and future research considerations.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116008},
doi = {10.1016/j.ab.2025.116008},
pmid = {41202947},
issn = {1096-0309},
abstract = {Dietary restriction of the sulfur amino acids methionine and cysteine (sulfur amino acid restriction [SAAR]) is a well-established paradigm for delaying disease onset and the aging process in several experimental models. In vivo, SAAR's anti-aging effects appear to be mediated by decreased growth hormone/insulin-like growth factor-1 (GH/IGF-1) signaling, along with improvement in insulin sensitivity and overall metabolic health. SAAR-fed animals also exhibit reduced regional and total adiposity, as well as oxidative stress and inflammation. Recent studies suggest that SAAR improves cognition, induces significant changes in gut microbiome composition, and that its benefits may depend on the age at which the intervention begins. In humans, observational studies have shown that higher plasma total cysteine levels are positively correlated with adiposity, insulin resistance, and an increased incidence of diabetes. Likewise, high dietary methionine and cysteine intake has been linked to increased risk of cardiovascular disease and diabetes-related mortality. Human dietary intervention studies have only been partly successful in translating the benefits of SAAR, and practical challenges for implementation remain to be addressed. This review summarizes recent advances in the SAAR field and discusses its translational potential for promoting metabolic health and reducing the risk of age-related diseases.},
}

@article {pmid41202881,
year = {2025},
author = {Hasan, MN and Wang, H and Luo, W and Du, Y and Xiong, L and Gu, L and Li, T},
title = {A Gly-β-muricholic acid and FGF15 combination therapy synergistically reduces "humanized" bile acid pool toxicity in cholestasis mice.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100936},
doi = {10.1016/j.jlr.2025.100936},
pmid = {41202881},
issn = {1539-7262},
abstract = {Hydrophobic bile acid-mediated hepatobiliary injury is a major driver of cholestasis progression. Most anti-cholestasis treatments being tested clinically are based on a single agent, which does not always sufficiently alleviate bile acid toxicity to slow disease progression. This study investigates a therapeutic strategy of combining glycine-conjugated β muricholic acid (Gly-βMCA) and fibroblast growth factor-15 (FGF15) to alleviate bile acid hepatobiliary toxicity in Cyp2c70 KO mice that lack endogenous muricholic acid (MCA) synthesis and have a "humanized" hydrophobic bile acid pool composition. The effects of the single and combination treatments on bile acid metabolism, liver injury, and gut microbiome were investigated in female Cyp2c70 KO mice with progressive cholangiopathy and portal fibrosis. While all three treatments significantly reduced biochemical and histologic features of liver injury, the Gly-βMCA and FGF15 combination achieved a remarkably higher reduction in both bile acid pool size and hydrophobicity than either single treatment. Mechanistically, this resulted from synergistically increased biliary hydrophilic MCA species derived from Gly-βMCA, inhibited intestine endogenous bile acid absorption by Gly-βMCA, and repressed cholesterol 7α-hydroxylase (CYP7A1) by FGF15, which counteracted the undesirable farnesoid x receptor (FXR) antagonism activity of Gly-βMCA. Furthermore, a hydrophobic bile acid pool in Cyp2c70 KO mice was associated with markedly reduced beneficial Lactobacillaceae family bacteria abundance, which was enriched by Gly-βMCA and the combination treatments. In conclusion, the Gly-βMCA and FGF15 combination shows enhanced efficacy in decreasing humanized bile acid pool size and hydrophobicity and holds potential as a therapeutic strategy to decrease bile acid burden in cholestasis.},
}

@article {pmid41202606,
year = {2025},
author = {Li, Y and Xiao, H and Liu, L and Jiang, F and Yu, E},
title = {Multi-omics reveals the mechanism of environmental concentration of microcystin-LR-induced muscle damage and nutrient loss and the role of gut-muscle axis in Nile tilapia.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119352},
doi = {10.1016/j.ecoenv.2025.119352},
pmid = {41202606},
issn = {1090-2414},
abstract = {Microcystin-LR (MC-LR), a prevalent and highly potent cyanobacterial toxin, is generated during the outbreaks of these blooms. Despite its prevalence, there is a scarcity of information regarding the chronic effects and underlying molecular mechanisms of MC-LR at environmentally relevant concentrations on muscular toxicity in fish. Hence, we assessed the muscular toxicity of chronic MC-LR exposure via histological and biochemical analyses and delved into the underpinning mechanisms via holistic multi-omics approaches of gut microbiome, serum metabolome, muscle transcriptome and metabolome in Nile tilapia. After 60 days of MC-LR exposure, 30 μg/L MC-LR exposure significantly triggered muscular toxicity, as illustrated by decreased nutrient value, reduced myofiber diameter and sarcomere length, and diffuse dissolution of myofibrils. Transcriptomic and metabolomic analyses of muscle revealed that MC-LR exposure altered antioxidant status, protein turnover, amino acid metabolism, nucleotide synthesis and breakdown, and lipid metabolism regulation, leading to oxidative stress, inflammation response, apoptosis, decreased protein deposition and inhibited myofiber growth of Nile tilapia. Furthermore, MC-LR exposure perturbed the intestinal microbiota composition and compromised the integrity of the intestinal barrier, resulting in increased toxicity-related metabolites such as lipopolysaccharide (LPS), phenol and phenylacetic acid entering the muscle through the bloodstream, promoting muscle injury. These results provided new insight into the underlying biomolecular mechanisms and potential roles of the gut-muscle axis in MC-LR-induced muscular toxicity in aquatic animals.},
}

@article {pmid41202528,
year = {2025},
author = {Hu, X and Wu, M and Zhao, B and Xu, T and Jia, Z and Zhao, X},
title = {Construction of a succession model for the microbiome in water from submerged corpses based on single-molecule real-time sequencing.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103378},
doi = {10.1016/j.fsigen.2025.103378},
pmid = {41202528},
issn = {1878-0326},
abstract = {Decomposition of corpses in aquatic environments is regulated by multiple factors, and traditional methods for estimating the postmortem submerged interval (PMSI) have clear limitations. To explore the microbial succession patterns in the water of submerged corpses and their potential application in PMSI estimation, this study submerged rat carcasses in both river water and tap water, collecting water samples on days 0, 2, 6, 9, 14, 20, 27, 40, 54, and 70 postmortem. The microbial succession dynamics in the water were analyzed using single-molecule real-time sequencing. The results indicated that, although the response patterns to decomposition differed between the two water sources, key microorganisms common to various decomposition stages were identified, suggesting their important role in the process. This study characterized the microbial community succession trajectory at the species level and identified several species with potential for PMSI indication. Based on this, we constructed a simple random forest prediction model. During the 70-day decomposition period, the mean absolute errors (MAE) of the river water model and the tap water model were 5.8745 days and 4.8599 days, respectively. This research elucidates the microbial community succession patterns induced by corpse submersion in water, constructs a methodological framework for PMSI estimation based on water microbiomes, and provides crucial support for the development of more versatile PMSI inference models.},
}

@article {pmid41202150,
year = {2025},
author = {Champagne-Jorgensen, K and Gommerman, JL},
title = {Two of a kind, one with MS: Gut microbes tip the balance.},
journal = {Science immunology},
volume = {10},
number = {113},
pages = {eaed4910},
doi = {10.1126/sciimmunol.aed4910},
pmid = {41202150},
issn = {2470-9468},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Animals ; *Multiple Sclerosis/immunology/microbiology ; Mice ; Fecal Microbiota Transplantation ; },
abstract = {An MS twin study links ileal Lachnospiraceae to spontaneous CNS autoimmunity in mice receiving a human microbiome transplant.},
}

*Gastrointestinal Microbiome/immunology
Humans
Animals
*Multiple Sclerosis/immunology/microbiology
Mice
Fecal Microbiota Transplantation

@article {pmid41202107,
year = {2025},
author = {Pérez-Trejo, A and Aguirre-Macedo, ML and Banaszak, AT and García-Maldonado, JQ},
title = {Differentiation of the bacterial communities associated with Orbicella faveolata across different growth conditions and life-cycle stages.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335445},
doi = {10.1371/journal.pone.0335445},
pmid = {41202107},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Anthozoa/microbiology/growth & development ; *Life Cycle Stages ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {The coral microbiome can strongly influence coral health, development, and resilience. While larval settlement is fundamental for coral restoration efforts using assisted larval propagation, post-settlement survival remains a major challenge. The study of lab-bred Orbicella faveolata settlers (LBOFS) microbiome has been proposed due to its potential role in coral adaptation processes. However, there is limited information about LBOFS bacterial communities and comparisons between different growth conditions and life-cycle stages have not been conducted. Using 16S rRNA high-throughput sequencing, we analyzed the structure and composition of LBOFS-associated bacteria and compared them to those from outplanted LBOFS and wild settlers. We also compared the microbiomes of settlers to adult colonies. The LBOFS bacterial community was composed of 4224 ASVs with the Orders Kiloniellales, Rhodobacterales, Cytophagales, Cyanobacteriales, and Flavobacteriales being the most abundant across the samples, with a rare biosphere consisting of 44.6% relative abundance. A Principal Coordinates Analysis and a PERMANOVA indicated significantly different bacterial community structures based on settler growth conditions and life-cycle stage. Linear discriminant analysis Effect Size analysis identified specific taxa whose differential abundances contributed to the observed differences. For settler growth conditions, the differences were mainly due to the Order Cyanobacteriales for LBOFS, SAR202 clade for outplanted settlers, and Microtrichales for wild samples. Statistical analysis of functional prediction showed significant differences only in nitrogen fixation for LBOFS. For life-cycle stage, LEfSe revealed that the Orders Cytophagales and Cyanobacteriales exhibited the highest differential abundances in adults and settlers, respectively. Functional prediction revealed that nitrogen fixation and oxygenic photoautotrophy were more enriched in settlers, whereas nitrate reduction and anaerobic chemoheterotrophy were more enriched in adults. This study highlighted the bacterial taxa and predicted metabolic processes that could potentially contribute to coral settler functioning, providing a valuable baseline for future research to enhance their survival rates using probiotics.},
}

Animals
*Microbiota/genetics
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Anthozoa/microbiology/growth & development
*Life Cycle Stages
Phylogeny
High-Throughput Nucleotide Sequencing

@article {pmid41202104,
year = {2025},
author = {Huang, Y and Tang, T and Dai, X and Sun, F},
title = {Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013691},
doi = {10.1371/journal.pcbi.1013691},
pmid = {41202104},
issn = {1553-7358},
abstract = {Understanding microbial interactions is fundamental for exploring population dynamics, particularly in microbial communities where interactions affect stability and host health. Generalized Lotka-Volterra (gLV) models have been widely used to investigate system dynamics but depend on absolute abundance data, which are often unavailable in microbiome studies. To address this limitation, we introduce an iterative Lotka-Volterra (iLV) model, a novel framework tailored for compositional data that leverages relative abundances and iterative refinements for parameter estimation. The iLV model features two key innovations: an adaptation of the gLV framework to compositional constraints and an iterative optimization strategy combining linear approximations with nonlinear refinements to enhance parameter estimation accuracy. Using simulations and real-world datasets, we demonstrate that iLV surpasses existing methodologies, such as the compositional LV (cLV) and the generalized LV (gLV) model, in recovering interaction coefficients and predicting species trajectories under varying noise levels and temporal resolutions. Applications to the lynx-hare predator-prey, Stylonychia pustula-P. caudatum mixed culture, and cheese microbial systems revealed consistency between predicted and observed relative abundances showcasing its accuracy and robustness. In summary, the iLV model bridges theoretical gLV models and practical compositional data analysis, offering a robust framework to infer microbial interactions and predict community dynamics using relative abundance data, with significant potential for advancing microbial research.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201910,
year = {2025},
author = {Kulal, R and Touseef Khan, M and Bhaskarrao Borse, B and Peddha, MS},
title = {Effect of encapsulated spice oleoresins on chronic unpredictable mild stress-induced depression and gut microbiome modulation in mice model.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2025.2582520},
pmid = {41201910},
issn = {1476-8305},
abstract = {Depression affects millions globally, prompting the search for novel treatments. Natural compounds like spice oleoresins show promise due to their bioactive constituents. This study explores the use of Hydroxypropyl-beta-cyclodextrin (HPBCD) for nano-encapsulation to enhance the efficacy of pepper, turmeric, and chilli oleoresins in alleviating depression in a mice model. Chronic unpredictable mild stress (CUMS) was induced for 28 days, followed by administering nano-encapsulated oleoresins (25 mg/kg). Behavioural analyses revealed improved activity, while neurochemical studies showed increased serotonin and dopamine levels with reduced monoamine oxidase (MAO) activity. Western blot highlighted changes in BDNF, supported by histopathological evidence of neuroprotection. Biochemical assays indicated reduced oxidative stress, acetylcholinesterase activity, and enhanced catalase and superoxide dismutase levels. 16S rRNA sequencing revealed improved gut microbiota, with increased beneficial bacteria. Notably, nano-encapsulated chilli oleoresin exhibited the highest efficacy. These findings support the multi-targeted potential of nano-encapsulated spice oleoresins as complementary treatments for depression, addressing neurobiological and gut-related factors.},
}

@article {pmid41201906,
year = {2025},
author = {Gao, Y and Zhu, T and Zhang, Z and Hu, H and Wang, Q and Liu, H and Xiong, L},
title = {Characterization of a Cold-Active Xylanase from Paenibacillus sp. XP01, and Its Application in Hydrolyzing Alkali-Pretreated Corncob Residues.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08788},
pmid = {41201906},
issn = {1520-5118},
abstract = {Xylan, a key hemicellulose in agricultural byproducts, is significantly underutilized in biorefineries. The human gut microbiome, with its diverse enzymes, holds great potential for biocatalyst discovery. In this study, Paenibacillus sp. XP01, a xylan-degrading strain, was isolated from human feces. Genomic analysis identified a GH11 endo-β-1,4-xylanase, designated Xyn157, which exhibited a cold-active property. It retained 47% residual activity at 0 °C and 72% at 4 °C. It also exhibited catalytic activity against insoluble xylan in corncob. Enzymatic profiling confirmed its endoacting mode, with xylotriose as the minimum substrate and branched chains impairing efficiency. Xyn157 hydrolyzed alkali-pretreated corncob residues (ACR) to produce xylo-oligosaccharide (XOS), with a yield of 6.4% (w/w). In vitro fermentation of Xyn157-treated ACR, which produced hydrolysis products of ACR (CRH), significantly promoted the growth of beneficial bacteria (e.g., Bifidobacterium, Ligilactobacillus), suppressed pathogens (e.g., Enterobacter and Klebsiella), and boosted short-chain fatty acid (SCFA) production compared to the ACR group. These findings highlight Xyn157's potential to convert insoluble xylan in ACR into functional prebiotics, expanding its applications in waste-to-prebiotic bioprocessing.},
}

@article {pmid41201826,
year = {2025},
author = {Sorger, Z and Sengupta, P and Beier-Heuchert, K and Bautor, J and Parker, JE and Kemen, E and Doehlemann, G},
title = {GH25 lysozyme mediates tripartite interkingdom interactions and microbial competition on the plant leaf surface.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {45},
pages = {e2510124122},
doi = {10.1073/pnas.2510124122},
pmid = {41201826},
issn = {1091-6490},
support = {390686111//Deutsche Forschungsgemeinschaft (DFG)/ ; DECRyPT//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Arabidopsis/microbiology ; *Muramidase/metabolism/genetics ; *Plant Leaves/microbiology ; Plant Diseases/microbiology ; Microbiota ; Oomycetes ; },
abstract = {Microbial communities inhabiting plants have emerged as crucial factors in regulating plant health and defense against disease-causing pathogens. The yeast Moesziomyces bullatus ex. Albugo (MbA) on Arabidopsis produces a glycoside hydrolase 25 (GH25) protein that regulates the leaf microbiome by antagonizing the pathogenic oomycete Albugo laibachii. Applying MbA or GH25 rescued Arabidopsis thaliana shoot fresh weight under A. laibachii infection, highlighting their crop protection potential. Interaction assays revealed no antagonistic activity of GH25 against other plant pathogenic oomycetes or fungi besides A. laibachii. We identified a community of bacteria closely associated with A. laibachii. Three of these bacteria are inhibited by GH25 and one of them, Curtobacterium sp. could override the inhibition of A. laibachii by MbA. This points to a tripartite antagonism where Curtobacterium and A. laibachii protect each other from MbA. Moreover, Curtobacterium selectively inhibits other A. laibachii-associated bacteria not targeted by MbA but that themselves suppress A. laibachii. This study uncovers an interkingdom network where GH25 lysozyme shapes microbial interactions between yeast, oomycete, and associated bacteria.},
}

*Arabidopsis/microbiology
*Muramidase/metabolism/genetics
*Plant Leaves/microbiology
Plant Diseases/microbiology
Microbiota
Oomycetes

@article {pmid41201785,
year = {2025},
author = {Baker, SG and Morton, CO and Green, H},
title = {The impact of freezing temperatures on soft tissue and microbial decomposition using human and porcine remains: a pilot study.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {41201785},
issn = {1556-2891},
abstract = {Environmental factors such as temperature, vertebrate and invertebrate activity and microbial succession patterns are important variables driving the decomposition process. However, the effects of low temperatures, specifically freezing on how a body decomposes are less understood. This pilot project aimed to determine the taphonomic effects of freezing on morphological changes during decomposition and the microbiome in an Australian context. Two human donors (one frozen, one non-frozen) and two frozen and two non-frozen Sus scrofa (pig) carcasses (n = 4) were allowed to decompose on the surface of woodlands for 12-weeks during summer 2017. Visual morphological changes were recorded, and microbial swabs were collected at regular intervals and analysed via real-time PCR to assess differences in bacterial community structure. Results indicated clear differences in decomposition patterns between frozen and non-frozen remains. Frozen remains were slow to enter 'early' decomposition but first to skeletonise. Microbial results suggest that patterns in community structure between bacteria may indicate if a body has been frozen at or around the time of death. This research suggests that quantifying the microbiome present during the fresh and early stages of decomposition and noting observations of an outside-in decomposition pattern may be a useful tool in identifying if remains have experienced extreme cold temperatures at the time of death. This knowledge could improve approaches to PMI estimation, particularly if the remains have experienced a freeze-thaw event after death.},
}

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201719,
year = {2025},
author = {Gautam, P and Vishwakarma, RK and Nath, M and Nath, G and Pathak, A},
title = {Microbiota Dysbiosis in Amyotrophic Lateral Sclerosis: A Systematic Review of Human Studies.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {10},
pmid = {41201719},
issn = {1559-1182},
mesh = {*Amyotrophic Lateral Sclerosis/microbiology/complications ; Humans ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron degeneration. Despite intensive research, its pathogenesis remains poorly understood. Recent insights suggest a pivotal role of the gut microbiota in modulating neuroinflammation and neurodegeneration via the gut-brain axis. This systematic review aims to synthesize clinical evidence on gut microbiota dysbiosis in ALS, exploring microbial and metabolic alterations and their associations with disease progression and severity. A comprehensive literature search was conducted across PubMed, Embase, Scopus, Web of Science, and other databases up to May 10, 2024, adhering to PRISMA 2020 guidelines. Eighteen eligible human studies were selected based on predefined inclusion criteria. Data on microbial diversity, taxonomic shifts, metabolite profiles, and clinical correlations were extracted and assessed using a modified Newcastle-Ottawa Scale. Most studies reported altered microbial diversity, reduced butyrate-producing bacteria (e.g., Faecalibacterium, Roseburia), and increased pro-inflammatory taxa (e.g., Escherichia coli, Bacteroides) in ALS. Integrated microbiome-metabolome analyses revealed disruptions in SCFAs, bile acids, and lipid metabolism, some correlating with ALSFRS-R scores and cognitive impairment. Although some studies showed minimal or no differences, the overall evidence supports a link between dysbiosis and ALS pathophysiology. Probiotic trials demonstrated limited efficacy, highlighting the need for targeted, patient-specific interventions. Gut microbiota dysbiosis is increasingly recognized as a contributor to ALS progression. However, methodological variability, small sample sizes, and limited longitudinal data restrict definitive conclusions. Future research should employ standardized, multi-omics approaches and larger cohorts to clarify causal links and develop microbiome-informed diagnostics and therapies for ALS.},
}

*Amyotrophic Lateral Sclerosis/microbiology/complications
Humans
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome/physiology

@article {pmid41201258,
year = {2025},
author = {Zhang, Y and Wang, M and Sun, Y and Gao, H and Su, X},
title = {Function inference of million-scale microbiomes using multi-GPU acceleration.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0207225},
doi = {10.1128/spectrum.02072-25},
pmid = {41201258},
issn = {2165-0497},
abstract = {Amplicon sequencing enables taxonomic profiling of microbial communities but offers limited insight into their functional potential. Existing tools such as Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) infer functions through phylogenetic placement and ancestral state reconstruction; however, these methods are computationally intensive and inefficient for large-scale data sets. To address these challenges, we introduce microbiome graphics processing unit (GPU)-based function inference (MGFunc), an ultra-high-throughput framework for microbiome functional inference leveraging multi-GPU acceleration. MGFunc transforms functional prediction for amplicons into standardized matrix multiplication using a pre-constructed genomic content network. It further integrates split data loading, matrix partition, and dynamic scheduling across multiple GPUs, enabling scalable, batch-wise analysis of millions of samples under limited GPU memory and system random access memory (RAM). Compared to PICRUSt2, MGFunc achieves speedups of up to several hundred thousand times, completing the functional interpretation of one million samples within one minute by four GPUs on a single server. This work provides a highly efficient and low-latency solution for ultra-large microbiome data sets functional inference, paving the way for global-scale microbiome studies. The MGFunc software is freely accessible at https://github.com/qdu-bioinfo/MGFunc.IMPORTANCEUnderstanding what microbes do-their functions-is essential for studying health, disease, agriculture, and the environment. While cost-effective sequencing methods like 16S rRNA gene analysis are widely used, they do not directly reveal microbial functions. Existing tools that predict these functions from 16S data are often too slow for today's large studies involving hundreds of thousands of samples. In this work, we developed microbiome graphics processing unit (GPU)-based function inference (MGFunc), a new method that predicts microbial functions quickly and accurately by using GPUs and a streamlined mathematical approach. MGFunc can analyze over one million samples in under a minute, making it one of the fastest tools available. This enables researchers to study the functional potential of microbial communities on a truly global and population scale.},
}

@article {pmid41201243,
year = {2025},
author = {Nash, J and Tremble, K and Schadt, C and Cregger, MA and Bryan, C and Vilgalys, R},
title = {Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028525},
doi = {10.1128/msystems.00285-25},
pmid = {41201243},
issn = {2379-5077},
abstract = {UNLABELLED: The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller "active core" subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

IMPORTANCE: Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.},
}

@article {pmid41201238,
year = {2025},
author = {Rees, NP and Conway, J and Dugan, B and Amir, SS and Parker, A and Carding, SR and Duggal, NA},
title = {Defining Microbiota-Derived Metabolite Butyrate as a Senomorphic: Therapeutic Potential in the Age-Related T Cell Senescence.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70257},
doi = {10.1111/acel.70257},
pmid = {41201238},
issn = {1474-9726},
abstract = {Advancing age is accompanied by an accumulation of senescent T cells that secrete pro-inflammatory senescence-associated secretory phenotype (SASP) molecules. Gut-microbiota-derived signals are increasingly recognised as immunomodulators. In the current study, we demonstrated that ageing and the accumulation of senescent T cells are accompanied by a reduction in microbial-derived short-chain fatty acids (SCFAs). Culturing aged T cells in the presence of butyrate suppresses the induction of a senescence phenotype and inhibits the secretion of pro-inflammatory SASP factors, such as IL6 and IL8. Administration of faecal supernatants from young mice rich in butyrate prevented in vivo accumulation of senescent spleen cells in aged mice. The molecular pathways governing butyrate's senomorphic potential include a reduced expression of DNA damage markers, lower mitochondrial ROS accumulation, and downregulation of mTOR activation, which negatively regulates the transcription factor NFκB. Our findings establish butyrate as a potent senomorphic agent and provide the evidence base for future microbiome restitution intervention trials using butyrate supplements for combating T cell senescence, ultimately reducing inflammation and combating age-related pathologies to extend lifelong health.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41201222,
year = {2025},
author = {Zheng, Y and Gao, Z and Sun, L and Shi, J and Song, J and Ye, W},
title = {Calcium and Gastrointestinal Disorders: Mechanistic Insights and Therapeutic Interventions.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {39241},
doi = {10.31083/IJVNR39241},
pmid = {41201222},
issn = {0300-9831},
support = {ZA CACM 2024002//Clinical Research Project of the China Association of ChineseMedicine/ ; 2020SJZDXK13//Health Commission of Zhejiang Chinese Medical University Hangzhou Hospital of Traditional Chinese Medical/ ; },
mesh = {Humans ; *Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology ; *Calcium/metabolism ; Gastrointestinal Microbiome ; Receptors, Calcium-Sensing/metabolism ; Dietary Supplements ; *Calcium, Dietary/administration & dosage ; Hypocalcemia ; },
abstract = {Calcium plays a central role in gastrointestinal (GI) physiology through regulating smooth muscle contractility, acid secretion, epithelial barrier integrity, and immune signaling. The dysregulation of calcium homeostasis has been increasingly implicated in the pathogenesis of GI disorders, including colorectal cancer, inflammatory bowel disease, peptic ulcer, and pancreatitis. Specifically, aberrant calcium-sensing receptor (CaSR) signaling has emerged as a critical molecular mechanism in colorectal tumorigenesis; meanwhile, calcium-mediated pathways influence gastric acid production and intestinal motility. This review critically evaluated recent advances in calcium signaling within the GI tract, highlighting the crosstalk involved with the gut microbiota and the roles of downstream effectors, including transient receptor potential vanilloid type 6 and store-operated calcium entry. This review also examined the therapeutic implications of calcium supplementation across various GI conditions, including bioavailability challenges under different disease states and nutrient interactions involving vitamin D and phosphate. Our review further addresses the role of calcium in mucosal immunity, the clinical relevance of hypocalcemia in GI diseases, and the potential of microbiome-guided nutritional interventions. However, despite growing mechanistic insights, considerable gaps remain in understanding host-microbiota-calcium interactions, genotype-specific responses to calcium, and long-term clinical outcomes. Thus, future research should clarify the dose-response relationships, stratify patient populations by CaSR polymorphisms and microbiome profiles, and establish precision strategies for calcium-based interventions in digestive health.},
}

Humans
*Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology
*Calcium/metabolism
Gastrointestinal Microbiome
Receptors, Calcium-Sensing/metabolism
Dietary Supplements
*Calcium, Dietary/administration & dosage
Hypocalcemia

@article {pmid41200858,
year = {2025},
author = {Huang, Z and Brot, L and Fatouh, R and Bredon, M and Creusot, L and Lefèvre, A and Lamazière, A and Lefevre, JH and Emond, P and Planchais, J and Roux, X and Sokol, H and Rolhion, N},
title = {Saccharomyces boulardii CNCM I-745 mitigates antibiotic-induced gut microbiome functional alterations independently of the host.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2575924},
doi = {10.1080/19490976.2025.2575924},
pmid = {41200858},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Saccharomyces boulardii/physiology ; *Probiotics/pharmacology/administration & dosage ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Vancomycin/adverse effects ; Dysbiosis/chemically induced/microbiology ; Cytokines/metabolism ; Leukocytes, Mononuclear/drug effects/immunology ; Amoxicillin-Potassium Clavulanate Combination/adverse effects ; Intestinal Mucosa/microbiology/drug effects/immunology ; Bacteria/drug effects/genetics/classification/growth & development ; },
abstract = {The probiotic Saccharomyces boulardii CNCM I-745 (Sb) is widely prescribed to alleviate antibiotic-induced diarrhea, yet its mode of action, particularly its potential direct effects on the gut microbiome, remains incompletely defined. This study aimed to evaluate whether Sb can directly mitigate antibiotic-induced gut microbiota dysbiosis and influence downstream host immune response. Using both static (MiPro) and dynamic (SHIME[®]) in vitro gut microbiota models, we assessed the effects of Sb supplementation under antibiotic treatment with amoxicillin/clavulanic acid (AMC) or vancomycin (Van). Quantitative microbiome profiling integrated with targeted metabolomics showed that Sb helped stabilize bacterial biomass, partially preserved metabolic functions, and restored the production of immunoregulatory metabolites propionate and indole-3-propionic acid under AMC treatment. In addition, ex vivo exposure of primary human immune cells (PBMCs) and intestinal mucosal tissue to microbiota modulated by Sb led to a significant reduction in pro-inflammatory cytokine secretion compared to microbiota not supplemented with Sb. Collectively, these results support a beneficial role for S. boulardii CNCM I-745 in preserving directly gut microbiome function and supporting host immune homeostasis during antibiotic treatment, particularly under AMC exposure. Our findings advance the understanding of probiotic-antibiotic-gut microbiome interactions, thereby guiding future optimization of microbiome-targeted adjuvant therapies.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Saccharomyces boulardii/physiology
*Probiotics/pharmacology/administration & dosage
*Anti-Bacterial Agents/adverse effects/pharmacology
Vancomycin/adverse effects
Dysbiosis/chemically induced/microbiology
Cytokines/metabolism
Leukocytes, Mononuclear/drug effects/immunology
Amoxicillin-Potassium Clavulanate Combination/adverse effects
Intestinal Mucosa/microbiology/drug effects/immunology
Bacteria/drug effects/genetics/classification/growth & development

@article {pmid41200610,
year = {2025},
author = {Ur Rehman, M and Saeed, H and Omer, O and Tashfeen, S},
title = {Gut Microbiota-Directed Interventions in Type 2 Diabetes: A Systematic Review of Clinical Outcomes and Complication Risk.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95045},
pmid = {41200610},
issn = {2168-8184},
abstract = {Type 2 diabetes mellitus is increasingly recognized as a disorder not only of glucose metabolism but also of gut microbial imbalance, with emerging evidence suggesting a bidirectional link between microbiome composition and metabolic dysfunction. Recent randomized controlled trials and dietary interventions highlight that specific microbial taxa, such as butyrate-producing bacteria and Akkermansia muciniphila, play crucial roles in regulating insulin sensitivity, lipid metabolism, and systemic inflammation. Modulation of the gut-metabolic axis through probiotics, prebiotics, dietary strategies, and pharmacological agents demonstrates promising effects on glycemic control, cardiometabolic risk reduction, and attenuation of diabetes-related complications, though results vary across populations and intervention types. The variability in outcomes underscores the importance of personalized approaches, where baseline microbiota signatures may dictate therapeutic response. Despite encouraging findings, many studies remain limited by short duration, small sample size, and heterogeneity in microbiome analysis methods. This review synthesizes current evidence, highlights mechanistic insights linking microbial shifts to metabolic benefits, and identifies gaps in the literature. By doing so, it emphasizes the potential of microbiome-directed therapies as adjunctive strategies in the prevention and management of type 2 diabetes and its complications.},
}

@article {pmid41200544,
year = {2025},
author = {Cheng, J and Gao, Y and Lv, H and Li, J and Sun, X and An, T and Liu, H and Wang, J and Zhang, H and Wang, H and Zou, S and Fan, Z and Chen, Y},
title = {LGG/LAC-MMT combination mitigates AFB1-induced liver and intestinal injury in mice based on intestinal microbiota modulation.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1654294},
pmid = {41200544},
issn = {2297-1769},
abstract = {AFB1 induces hepatotoxicity and enterotoxicity. Lactobacillus acidophilus (LAC) and Lactobacillus rhamnosus (LGG), both belonging to LAB, have strong binding affinity for AFB1. Montmorillonite (MMT) not only adsorbs AFB1 but also serves as a carrier for LAB, thereby enhancing their colonization ability and prolonging their survival. Despite the unclear effects of LGG/LAC-MMT combination on AFB1-induced tissue injury and intestinal microbiota disruption, this study aimed to determine whether it could effectively alleviate tissue damage from AFB1 exposure and enhance LAB colonization capacity in mouse intestines. Separately, LGG (2 × 10[9] cfu/mL) and LAC (2 × 10[9] cfu/mL) were combined with MMT (0.5 mg/kg), and the AFB1-intoxicated mice were gavaged with the mixtures for 4 weeks. Findings suggested that LGG, LAC, and MMT supplementation restored oxidative stress and inflammatory caused by AFB1 to some degree. Furthermore, they altered the intestinal microbiota structure, enhancing the colonization ability of LABs, thereby alleviating liver and intestinal injury. The combination of LGG/LAC-MMT was more effective, especially LAC-MMT. Overall, LGG/LAC-MMT exhibits a synergistic effect and can effectively ameliorate AFB1-induced tissue injury and intestinal microbiota disorder.},
}

@article {pmid41200416,
year = {2025},
author = {Shunmugavelu, K and Shakthi Chakravarthy, BG and Priya, S},
title = {Determination of Fusobacterium nucleatum levels in patients with periodontal disease and oral squamous cell carcinoma.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc60},
pmid = {41200416},
issn = {2196-5226},
abstract = {INTRODUCTION: Fusobacterium (F.) nucleatum, a Gram-negative anaerobic bacterium, has been implicated in both periodontal disease and oral squamous cell carcinoma (OSCC). This review aims to evaluate the levels of F. nucleatum in patients with periodontal disease and OSCC, exploring its potential role in the pathogenesis.

METHODS: A comprehensive literature search was conducted across multiple databases, identifying studies that measured F. nucleatum levels in periodontal disease and OSCC tissues.

RESULTS: A higher prevalence of F. nucleatum exists in both periodontal disease and OSCC tissues compared to healthy controls.

CONCLUSION: It appears that there is a link between infection with F. nucleatum and the development of these oral diseases. Further research is warranted to elucidate the mechanisms underlying this association and to explore potential therapeutic interventions targeting F. nucleatum.},
}

@article {pmid41200410,
year = {2025},
author = {Danjuma, FY and Dashen, MM and Ngene, AC and Egbere, OJ},
title = {Prevalence of bacterial vaginosis and its associated risk factors among women of reproductive age attending Jos University Teaching Hospital, Plateau State, Nigeria.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc51},
pmid = {41200410},
issn = {2196-5226},
abstract = {INTRODUCTION: Bacterial vaginosis (BV) remains the most common cause of abnormal vaginal discharge due to altered vaginal flora with decreased Lactobacillus spp. and increased anaerobic bacteria. The objectives of this study were to establish the prevalence of BV and its risk factors among women of reproductive age.

METHOD: This cross-sectional descriptive survey was conducted among 220 non-pregnant women of reproductive age attending Jos University Teaching Hospital (JUTH) in Plateau state, north central Nigeria, between August 2021 and January 2022, in which 110 women were asymptomatic, and 110 women were symptomatic. Self-administered questionnaires were used to identify the sociodemographic status and predisposing factors of the participants. Positive BV diagnosis was made using the Nugent scoring system and bacterial species were identified on selective media. A descriptive analysis was performed using the Chi-squared test at a 95% confidence interval to determine the prevalence of BV and its associated risk factors.

RESULTS: The overall BV prevalence was 33.6%. BV was higher in symptomatic women (39.1%) than in asymptomatic women (28.2%). No correlation was found between BV and demography, knowledge, or health behaviour, including age, education, marital status, number of children, occupation, income, alcohol, tobacco smoking, or sexual as well as hygienic behaviour (p≥0.05). A total of 328 bacterial isolates from 16 species were identified, with Enterococcus (E.) faecalis being the most prevalent species, accounting for 39.3% of the total isolates. Other species isolated include Staphylococcus (S.) saprophyticus (13.6%), S. epidermidis (13.0%), S. aureus (4.7%), Streptococcus (Sr.) agalactiae (5.9%), Klebsiella (K.) pneumoniae (4.1%), Proteus (P.) mirabilis (2.4%), and Pseudomonas (P.) aeruginosa (3.6%) in the symptomatic group. S. saprophyticus (10,7%), S. aureus (3.8%), K. pneumoniae (2.5%), and P. aeruginosa (1.9%) were isolated in the asymptomatic group. P. mirabilis was not detected. Lactobacillus spp. were present but not dominant, with an overall prevalence of 8.2%.

CONCLUSION: The observed diversity in vaginal microbiota, particularly the higher prevalence of E. faecalis in asymptomatic women, suggests the complexity of microbial interactions. The low prevalence of Lactobacillus spp. indicates a potential risk for infections, while the presence of potentially pathogenic bacteria such as S. saprophyticus and Streptococcus agalactiae underscores the need for further research. Overall, the understanding of the vaginal microbiome is crucial for developing effective healthcare interventions for managing BV.},
}

@article {pmid41200380,
year = {2025},
author = {Mojgani, N and Bagheri, M and Ashique, S and Hosseini, SH and Hussain, A and Moharrami, M and Zahmatkesh, A and Moradi, M},
title = {Probiotics and postbiotics: a promising prophylactic measure for American foulbrood and European foulbrood diseases of honey bees.},
journal = {Veterinary research forum : an international quarterly journal},
volume = {16},
number = {10},
pages = {545-555},
pmid = {41200380},
issn = {2008-8140},
abstract = {American foulbrood (AFB) and European foulbrood (EFB) diseases caused by Paenibacillus larvae and Meliscococcus plutonius are prevalent honeybee brood diseases that pose significant economic challenges to the apiculture industry globally. Antibiotic treatment has led to the emergence of antibiotic-resistant strains, encouraging the search for alternative and safe measures to effectively control these diseases. Honeybee gut microbiomes have proven effects on all spectra of honeybee health by enhancing resistance to several diseases via immune modulation and the production of different antimicrobial metabolites. The major part of the gut microbiota is identified as probiotic bacteria, which are live microorganisms that, when administered in adequate amounts, confer health benefits to the host. Probiotics have shown promising health benefits for honeybees. Honeybee gut probiotics provide protection via the production of different metabolites (postbiotics), such as hydrogen peroxide, vitamins, organic acids, free fatty acids, bacteriocins, neurotransmitters, secreted bio-surfactants, and reactive oxygen species. Vast numbers of these gut bacteria and their postbiotics have wide-spectrum antibacterial effects on AFB and EFB. This review highlights the significance of the honeybee gut microbial community, its probiotic potency, and the role of postbiotic metabolites as safe prophylactic measures for preventing AFB and EFB diseases in honeybees.},
}

@article {pmid41200350,
year = {2025},
author = {Mohammadzadeh, P and Samadi, N and Mohammadi, B},
title = {Revolutionizing oronasal fistula treatment in Felis silvestris: Integrating bioengineered solutions and microbiome insights for enhanced healing.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {4775-4788},
pmid = {41200350},
issn = {2218-6050},
mesh = {Male ; Animals ; Cats ; Microbiota ; *Oral Fistula/veterinary/therapy ; Wound Healing ; Tissue Scaffolds ; Bioengineering ; Polyethylene Glycols ; },
abstract = {BACKGROUND: Oronasal fistulas (ONFs) present significant therapeutic challenges in veterinary medicine, particularly in patients with comorbidities, such as chronic kidney disease. This case report demonstrates an innovative bioengineered approach for ONF repair in Felis silvestris that combines autologous biomaterials with microbiome analysis.

CASE DESCRIPTION: A 15-year-old male European wildcat with a chronic traumatic ONF (11 × 8 mm) and concurrent International Renal Interest Society Stage 2 chronic kidney disease received a customized implant composed of autologous platelet-rich fibrin (PRF), bone marrow aspirate, and a 3D-printed polyethylene glycol diacrylate (PEGDA) scaffold. PEGDA was selected for its high biocompatibility and rapid photopolymerization. Healing was monitored via computed tomography imaging and 16S rRNA sequencing. The results demonstrated significant microbial dysbiosis post-injury (Shannon index: 5.2 ± 0.3 vs. 3.1 ± 0.4; p < 0.05), with opportunistic pathogen enrichment (Enterococcus faecalis: 0.5% → 12.8%). Antibiotics reduced the bacterial load by 99.9% (p < 0.001) but did not improve the closure rate (p = 0.89), underscoring the mechanical role of the scaffold.

CONCLUSION: The bioengineered implant facilitated complete mucosal integration and osteoconduction at the 10-month follow-up, demonstrating promise for complex ONF repair. However, the single-case design limits the generalizability.},
}

Male
Animals
Cats
Microbiota
*Oral Fistula/veterinary/therapy
Wound Healing
Tissue Scaffolds
Bioengineering
Polyethylene Glycols

@article {pmid41200191,
year = {2025},
author = {Qi, P and Gong, F and Leng, M and Wei, Z},
title = {Beneficial perspective on Staphylococcus epidermidis: a crucial species for skin homeostasis and pathogen defense.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674392},
pmid = {41200191},
issn = {1664-3224},
mesh = {*Staphylococcus epidermidis/immunology/physiology ; Humans ; *Homeostasis ; *Skin/microbiology/immunology ; Biofilms/growth & development ; Animals ; Microbiota/immunology ; *Staphylococcal Infections/immunology/microbiology ; Host-Pathogen Interactions/immunology ; },
abstract = {Human skin harbors a diverse microbiome that shapes immune function, protects against pathogens, and sustains tissue homeostasis. Among its dominant members, Staphylococcus epidermidis-a coagulase-negative staphylococcus-was long considered primarily an opportunistic pathogen, especially in the context of biofilm formation and implant-associated infections. However, emerging evidence reframes S. epidermidis as an active commensal, capable of controlling inflammation, supporting antimicrobial defenses, and stabilizing the cutaneous barrier. These dual roles are largely determined by its extensive strain-level heterogeneity and dynamic colonization strategies. Here, we review current progress in understanding the ecological versatility of S. epidermidis, with particular focus on its potential benefits, its diversity and colonization dynamics, and the balance of costs and benefits associated with its presence on human skin.},
}

*Staphylococcus epidermidis/immunology/physiology
Humans
*Homeostasis
*Skin/microbiology/immunology
Biofilms/growth & development
Animals
Microbiota/immunology
*Staphylococcal Infections/immunology/microbiology
Host-Pathogen Interactions/immunology

@article {pmid41200143,
year = {2025},
author = {Toh, QY and Kang, YN and Chee, SY and Chiu, HH},
title = {Effects of probiotics on patients with Prader-Willi syndrome: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1583574},
pmid = {41200143},
issn = {2296-861X},
abstract = {BACKGROUND: Prader-Willi Syndrome (PWS) involves growth, obesity, and behavioral challenges; probiotics may improve symptoms through the gut-brain axis, aiding treatment. This meta-analysis aimed to assess the impact of probiotic supplementation on individuals with PWS in terms of probiotic abundance, psycho-social outcomes, behavioral issues, and adverse events.

METHODS: We systematically conducted searches across PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, and the Web of Science. Our study included relevant randomized controlled trials (RCTs) published before February 2025. Two independent review authors evaluated study eligibility, extracted data, and assessed the risk of bias in the included studies. Data synthesis employed a random-effects model based on heterogeneity test results and was presented as the standardized mean difference (SMD) with a 95% confidence interval (CI).

RESULTS: A total of five RCTs were included. Probiotic supplementation led to a notable increase in the abundance of the Bifidobacterium genus (SMD 1.21; 95% CI, 0.02 to 2.39). Notably, 12 weeks of probiotics intake demonstrated a favorable trend on social engagement (SMD -0.68; 95% CI: -1.14 to -0.21; p = 0.004). In contrast, probiotics did not exhibit a significant influence on behavioural problems, and the safety of probiotics consumption was assured as there was no significant increase in gastrointestinal adverse events.

CONCLUSION: The validation of a probiotic treatment for PWS is currently an aspirational goal. Additional investigation is required to comprehensively comprehend the connection between PWS and the gut microbiome, as well as its potential ramifications for the disease phenotype.

PROSPERO, CRD42023416791.},
}