@article {pmid40389623,
year = {2025},
author = {Lloyd, L},
title = {Testosterone affects the vaginal microbiome in transgender men.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
pmid = {40389623},
issn = {1759-4820},
}

@article {pmid40389580,
year = {2025},
author = {Norkeweit, F and Schlicht, K and Rohmann, N and Hartmann, K and Türk, K and Settgast, U and Schulte, DM and Gilbert, F and Demetrowitsch, T and Brix, F and Bang, C and Franke, A and Schwarz, K and Laudes, M and Geisler, C},
title = {Healthy lifestyle, daytime sleepiness, and gut microbiome composition are determinants of functional strength in humans: a cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17378},
pmid = {40389580},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; Adult ; *Healthy Lifestyle/physiology ; *Hand Strength/physiology ; Sleep/physiology ; Aged ; },
abstract = {Age, metabolic inflammation, sleep patterns, lifestyle choices, and gut microbiome composition were investigated as factors influencing functional strength. The Northern German FoCus cohort subgroup (394 women, 233 men) was categorized into six groups based on weekly sports activity and handgrip strength (HGS) measurements. The analyses included anthropometric data, clinical biochemistry, medication, sleep duration, healthy lifestyle score (HLS), 16 S rRNA gut microbiota, serum and urine metabolomics, bile acids, and an adapted dietary inflammatory index (ADII) score. Associations were found between age, inflammation, and low functional strength, with sleep duration increasing the odds and a healthy lifestyle decreasing the risk. Urine metabolomics revealed differences in enrichment analyses. No significant differences were observed in the Chao1 and InVSimpson indices between the groups. At the genus level, some species were associated with daily sports activity, whereas others were associated with HGS measurements. Clostridium XIVa was found only in high- and medium-HGS groups, while Alistipes, Odoribacter, and Streptococcus decreased with activity. Thus, tailored lifestyle interventions may reduce the risk of poor functional strength.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Cross-Sectional Studies
Middle Aged
Adult
*Healthy Lifestyle/physiology
*Hand Strength/physiology
Sleep/physiology
Aged

@article {pmid40389439,
year = {2025},
author = {Zhang, YH and Dai, CS and Wang, YJ and Wang, WY and Qi, TT and Xia, MC and Zhou, G and Cui, YM},
title = {Intestinal permeability of N-acetylcysteine is driven by gut microbiota-dependent cysteine palmitoylation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4623},
pmid = {40389439},
issn = {2041-1723},
support = {82204515//National Natural Science Foundation of China (National Science Foundation of China)/ ; 7232262//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Acetylcysteine/metabolism/pharmacokinetics ; Animals ; Humans ; Rats ; Male ; Permeability ; *Cysteine/metabolism ; Lipoylation ; *Intestinal Mucosa/metabolism ; Rats, Sprague-Dawley ; Female ; Specific Pathogen-Free Organisms ; Germ-Free Life ; Intestinal Barrier Function ; },
abstract = {Trillions of intestinal microbiota are essential to the permeability of orally administered drugs. However, identifying microbial-drug interactions remains challenging due to the highly variable composition of intestinal flora among individuals. Using single-pass intestinal perfusion (SPIP) platform, we establish the microbiota-based permeability screening framework involving germ-free (GF) and specific-pathogen-free (SPF) rats to compare in-situ Peff-values and metabolomic profiles of 32 orally administered drugs with disputable classifications of permeability, prior to the verifications of bioorthogonal chemistry and LC-MS/MS. In contrast with SPF controls, N-Acetylcysteine (NAC) exhibits significantly increased permeability in GF rats, which is inversely related to reduced cysteine-3-ketosphinganine by Bacteroides. To further validate these microbiome features, we integrate clinical descriptors from a prospective cohort of 319 participants to optimize a 15-feature eXtreme Gradient Boosting (XGB) model, which reveal that cysteine palmitoylation by intestinal microbiota has significantly affected NAC permeability. By comparison of net reclassification improvement (NRI) index, this machine learning (ML) model of clinical prediction model encompassing intestinal microbial features outperforms other three commercial models in predicting NAC permeability. Here we have developed an intestinal microbiota-based strategy to evaluate uncharacterized NAC permeability, thus accounting for its discordant biopharmaceutics classification.},
}

*Gastrointestinal Microbiome/physiology
*Acetylcysteine/metabolism/pharmacokinetics
Animals
Humans
Rats
Male
Permeability
*Cysteine/metabolism
Lipoylation
*Intestinal Mucosa/metabolism
Rats, Sprague-Dawley
Female
Specific Pathogen-Free Organisms
Germ-Free Life
Intestinal Barrier Function

@article {pmid40389152,
year = {2025},
author = {Ma, R and Zhang, C and Zhang, Y and Tan, H and Zhang, Y and Li, Q and Bai, Y and Sun, X},
title = {The Impact of Respiratory Syncytial Virus on Asthma Development and Exacerbation.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2025.05.011},
pmid = {40389152},
issn = {1534-4436},
abstract = {Asthma is a chronic inflammatory disorder of the lower airways clinically characterized by recurrent wheezing, breathlessness, cough, and dyspnea, and is the most prevalent chronic disease among children and adolescents. Respiratory viral infections are implicated in asthma inception and exacerbation, with respiratory syncytial virus (RSV) emerging as a key contributor. RSV is a leading cause of acute lower respiratory tract infections (LRTIs), particularly infant bronchiolitis, and is associated with a type-2-biased immune response, diminished interferon activity, epithelial barrier dysfunction, and altered airway microbiome. While the causal relationship between RSV and asthma remains debated, early-life RSV LRTIs are increasingly recognized as a significant risk factor for recurrent wheezing and asthma-like symptoms in childhood. This review comprehensively evaluates existing evidence on the long-term respiratory outcomes of infant RSV infection, elucidates the pathophysiological mechanisms connecting RSV infection to asthma development-such as immune dysregulation, chronic airway inflammation, and gene-environment interplay-and highlights novel preventive strategies. Recent advancements, such as maternal RSV vaccines and long-acting monoclonal antibodies, demonstrate efficacy in reducing severe RSV disease burden and subsequent wheeze in high-risk infants. By bridging clinical observations with mechanistic insights, this review underpins the development of future clinical therapies.},
}

@article {pmid40389042,
year = {2025},
author = {Farahani, A and Farahani, A and Kashfi, K and Ghasemi, A},
title = {Inducible Nitric Oxide Synthase (iNOS): More Than an Inducible Enzyme? Rethinking the Classification of NOS Isoforms.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107781},
doi = {10.1016/j.phrs.2025.107781},
pmid = {40389042},
issn = {1096-1186},
abstract = {Nitric oxide (NO) is a critical signaling molecule synthesized from L-arginine by nitric oxide synthase (NOS). The three NOS isoforms-neuronal NOS (nNOS; NOS1), inducible NOS (iNOS; NOS2), and endothelial NOS (eNOS; NOS3)-have traditionally been classified as either constitutive (nNOS and eNOS) or inducible (iNOS). However, this binary classification oversimplifies their functions, particularly by neglecting the physiological roles of iNOS and misrepresenting its involvement in pathological processes. Increasing evidence demonstrates that all three isoforms can exhibit both constitutive and inducible expression. Notably, iNOS is constitutively expressed at low levels in several tissues, including blood, heart, bone marrow, lung, brain, spinal cord, retina, colonic mucosa, liver, ileum, skeletal muscle, epidermis, adipose tissue, endometrium, ovary, and kidney under normal physiological conditions, a form we refer to as constitutive iNOS (ciNOS). This basal expression contributes to essential functions such as heart rate regulation, respiratory exchange, and microbiome balance in the gut. Moreover, in certain pathological contexts, iNOS may exert protective rather than harmful effects, challenging the prevailing view that it is solely a pro-inflammatory mediator. Current drug development strategies targeting NOS are largely based on the outdated dichotomy of constitutive "physiologic" versus inducible "pathologic" isoforms, focusing primarily on iNOS inhibition. The failure of iNOS inhibitors in most clinical trials highlights the limitations of this approach. To address these gaps, we propose a revised nomenclature that incorporates both gene expression mode (constitutive vs. inducible) and discovery order, offering a more nuanced framework for understanding NOS isoforms in both health and disease.},
}

@article {pmid40389018,
year = {2025},
author = {Leekitcharoenphon, P and Bortolaia, V and Tornblom, VKW and Siriphap, A and Suthienkul, O and Borthong, J and Chonsin, K and Møller, FD and Avot, B and Otani, S and Aarestrup, FM},
title = {Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105765},
doi = {10.1016/j.meegid.2025.105765},
pmid = {40389018},
issn = {1567-7257},
abstract = {Antimicrobial resistance (AMR) is on one of the global priority challenges. This study explored the impact of diet alteration on AMR bacteria through metagenomic analysis during the annual vegetarian festival in Thailand in October 2019. The study investigated the effects of a 10-day shift from a regular to a vegetarian diet by collecting urban sewage from Nakhon Sawan, Surat Thani, and Bangkok before, during, and after the festival. Additionally, faecal samples from individuals in the northern city were analyzed. Using shotgun metagenomic sequencing, the samples were mapped against bacterial, AMR genes, and carbohydrate-active enzymes databases. The results revealed significant changes in AMR gene abundance and increased carbohydrate metabolism genes in sewage samples from all three cities during the festival. There was also a notable shift in the composition and diversity of bacterial species, particularly in the northern city. The total abundance of AMR genes increased during the vegetarian festival across all locations. This study highlights the correlation between a population's vegetarian diet and increased AMR in Thailand. It also demonstrates that metagenomic analysis of sewage can effectively assess the impact of dietary changes on bacterial communities and AMR at a population level, providing valuable insights for public health strategies.},
}

@article {pmid40388597,
year = {2025},
author = {Hwang, HG and Park, JW and Lee, HJ and Ko, MY and Ka, M and Lee, YK and Choi, J and In, SA and Lee, YE and Lee, S and Kim, MS and Kim, JY},
title = {Akkermansia muciniphila reverses neuronal atrophy in Negr1 knockout mice with depression-like phenotypes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2508424},
doi = {10.1080/19490976.2025.2508424},
pmid = {40388597},
issn = {1949-0984},
mesh = {Animals ; Mice, Knockout ; Mice ; *Depression/microbiology/genetics/pathology/therapy ; *Gastrointestinal Microbiome ; Atrophy ; Male ; *Akkermansia/physiology ; *Neurons/pathology ; Anxiety/microbiology ; Nucleus Accumbens/pathology/metabolism ; Hippocampus/pathology ; Mice, Inbred C57BL ; Phenotype ; *Nerve Tissue Proteins/genetics/metabolism ; },
abstract = {Genetic predispositions can shape the gut microbiome, which in turn modulates host gene expression and impacts host physiology. The complex interplay between host genetics and the gut microbiome likely contributes to the development of neuropsychiatric disorders, yet the mechanisms behind these interactions remain largely unexplored. In this study, we investigated the gut microbiota in Negr1 knockout (KO) mice, which exhibit anxiety- and depression-like behaviors, as NEGR1 (neuronal growth regulator 1) is a cell adhesion molecule linked to neuronal development and neuropsychiatric disorders. Our findings show significant early-life alterations in the gut microbiota composition of Negr1 KO mice, most notably a marked reduction in Akkermansia spp. along with reduced dendritic arborization and spine density in the nucleus accumbens (NAc) and the dentate gyrus (DG) of the hippocampus. Remarkably, daily administration of an Akkermansia strain isolated from wild-type mice reversed the neuronal structural abnormalities and ameliorated anxiety- and depression-like behaviors in Negr1 KO mice. Transcriptomic profiling revealed upregulation of mitochondrial genome-encoded genes in the NAc and hippocampus of Negr1 KO mice, along with a predisposition toward a pro-inflammatory state in the colon of Negr1 KO mice. The Akkermansia supplementation downregulated these mitochondrial genes in the NAc and hippocampus and upregulated genes involved in T cell activation and immune homeostasis in the colon. These findings demonstrate a novel gene-microbiome interaction in the pathophysiology of Negr1 KO mice, positioning Akkermansia spp. as a key mediator that improves neuronal atrophy and modulates anxiety- and depression-like behaviors. Our study provides compelling evidence for bidirectional interactions between host genetics and the gut microbiome in modulating neuropsychiatric phenotypes, offering new insights for addressing genetically influenced mental disorders.},
}

Animals
Mice, Knockout
Mice
*Depression/microbiology/genetics/pathology/therapy
*Gastrointestinal Microbiome
Atrophy
Male
*Akkermansia/physiology
*Neurons/pathology
Anxiety/microbiology
Nucleus Accumbens/pathology/metabolism
Hippocampus/pathology
Mice, Inbred C57BL
Phenotype
*Nerve Tissue Proteins/genetics/metabolism

@article {pmid40388589,
year = {2025},
author = {Lei, Z and Wang, H and Zhang, H and Liu, W and He, Z and Wang, Z and Zhang, H and Wang, Y and Tang, Y and Hu, C and Zhao, X},
title = {Sultr1;2-Mediated Recruitment of Selenium-Oxidizing Bacteria Promotes Plant Selenium Uptake.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c01540},
pmid = {40388589},
issn = {1520-5118},
abstract = {Plants can shape their root microbiome to promote growth and selenium uptake. Here, we used metagenomics, 16S high-throughput sequencing, and liquid chromatography-mass spectrometry (LC-MS) metabolomics assays to investigate the role of Sultr1;2, which is the major selenium transporter gene, in recruiting microbial communities to regulate soil selenium bioavailability and plant selenium uptake. Results shows that the overexpression of Sultr1;2 in tomato significantly enriched Methylobacterium genus. The isolated strains of Methylobacterium possess multiple plant-growth-promoting functions and selenium oxidation capability and inoculation with these strains increases soil selenium availability. The upregulated metabolites of Sultr1;2-overexpressing tomato were significantly enriched in the arginine and proline metabolism pathway. The key upregulated metabolites significantly improved the growth rate and selenium-oxidizing ability of Methylobacterium strains, and the combined addition of key upregulated metabolites and synthetic microbial community significantly increased soil selenium bioavailability and plant selenium uptake. This study provides insights into leveraging plant genetic engineering to identify key functional microbial communities for sustainable selenium-rich agricultural development.},
}

@article {pmid40388544,
year = {2025},
author = {Kohnert, E and Kreutz, C},
title = {Benchmarking Differential Abundance Tests for 16S microbiome sequencing data using simulated data based on experimental templates.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0321452},
doi = {10.1371/journal.pone.0321452},
pmid = {40388544},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Benchmarking ; Computer Simulation ; Humans ; *Metagenomics/methods ; Computational Biology/methods ; },
abstract = {Differential abundance (DA) analysis of metagenomic microbiome data is essential for understanding microbial community dynamics across various environments and hosts. Identifying microorganisms that differ significantly in abundance between conditions (e.g., health vs. disease) is crucial for insights into environmental adaptations, disease development, and host health. However, the statistical interpretation of microbiome data is challenged by inherent sparsity and compositional nature, necessitating tailored DA methods. This benchmarking study aims to simulate synthetic 16S microbiome data using metaSPARSim (Patuzzi I, Baruzzo G, Losasso C, Ricci A, Di Camillo B. MetaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics. 2019;20:416. https://doi.org/10.1186/s12859-019-2882-6 PMID: 31757204) MIDASim (He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. Available from: https://doi.org/10.1101/2023.03.23.533996), and sparseDOSSA2 (Ma S, Ren B, Mallick H, Moon YS, Schwager E, Maharjan S, et al. A statistical model for describing and simulating microbial community profiles. PLOS Comput Biol. 2021;17(9):e1008913. https://doi.org/10.1371/journal.pcbi.1008913 PMID: 34516542) , leveraging 38 real-world experimental templates (S3 Table) previously utilized in a benchmark study comparing DA tools. These datasets, drawn from diverse environments such as human gut, soil, and marine habitats, serve as the foundation for our simulation efforts. We employ the same 14 DA tests that were previously used with the same experimental data in benchmark studies alongside 8 DA tests that were developed subsequently. Initially, we will generate synthetic data closely mirroring the experimental datasets, incorporating a known truth to cover a broad range of real-world data characteristics. This approach allows us to assess the ability of DA methods to recover known true differential abundances. We will further simulate datasets by altering sparsity, effect size, and sample size, thus creating a comprehensive collection for applying the 22 DA tests. The outcomes, focusing on sensitivities and specificities, will provide insights into the performance of DA tests and their dependencies on sparsity, effect size, and sample size. Additionally, we will calculate data characteristics (S1 and S2 Table) for each simulated dataset and use a multiple regression to identify informative data characteristics influencing test performance. Our prior study, where we used simulated data without incorporating a known truth, demonstrated the feasibility of using synthetic data to validate experimental findings. This current study aims to enhance our understanding by systematically evaluating the impact of known truth incorporation on DA test performance, thereby providing further information for the selection and application of DA methods in microbiome research.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Benchmarking
Computer Simulation
Humans
*Metagenomics/methods
Computational Biology/methods

@article {pmid40388498,
year = {2025},
author = {Becker, MV and Accoti, A and Abu, AEI and Vulcan, J and Sylla, M and Khanipov, K and Dickson, LB},
title = {Reduced microbe abundance in an urban larval development container increases Aedes aegypti susceptibility to Zika virus.},
journal = {PLoS pathogens},
volume = {21},
number = {5},
pages = {e1013154},
doi = {10.1371/journal.ppat.1013154},
pmid = {40388498},
issn = {1553-7374},
abstract = {Aedes aegypti mosquitoes are a major vector of arboviruses that oviposit in both artificial containers (i.e., buckets, tires, cans) and natural containers (i.e., coconut husks, tree holes). These diverse container types will seed the larvae microbiome with differing bacterial communities. While the larval microbiome has been shown to alter adult susceptibility to arboviruses including dengue (DENV) and Zika virus (ZIKV), it is not known if exposure to different bacterial communities found between container types impacts adult Ae. aegypti interactions with arboviruses. To address this, rainwater was collected from an artificial container (plastic buckets) and a natural container (coconut husks) from three different collection sites and the microbiomes were preserved. Larval exposure to plastic bucket-derived microbiomes resulted in adults with increased susceptibility to ZIKV compared to larval exposure to coconut husk-derived microbiomes from all three collection sites, indicating that the container type, independent of collection environment, drives variation in adult susceptibility to ZIKV. 16S amplicon sequencing of larvae exposed to the preserved microbiomes revealed that bacterial community structure differed between plastic bucket and coconut husk derived communities at each collection site, but a conserved plastic- or coconut-derived bacterial community across collection sites was not identified. However, water from coconut husks had significantly more total bacterial abundance than water from plastic buckets. Normalization of bacterial loads between container types resulted in similar ZIKV infection rates. Together, these data suggest that larval exposure to specific container type-associated microbiomes alters adult susceptibility to ZIKV, largely driven by differences in total bacterial density between container types. Results from this study will help understand how the urbanization-driven expansion of Ae. aegypti into new/different oviposition sites might affect arbovirus susceptibility.},
}

@article {pmid40388308,
year = {2025},
author = {Wang, S and Kong, F and Dai, D and Li, C and Hao, Y and Wang, E and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Deterministic succession patterns in the rumen and fecal microbiome associate with host metabolic shifts in peripartum dairy cattle.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf042},
pmid = {40388308},
issn = {2047-217X},
support = {2022YFD1301400//National Key Research and Development Program/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Female ; *Peripartum Period/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Pregnancy ; },
abstract = {BACKGROUND: Metabolic disorders in peripartum ruminants affect health and productivity, with gut microbiota playing a key role in host metabolism. Therefore, our study aimed to characterize the gut microbiota of peripartum dairy cows to better understand the relationship between metabolic phenotypes and the rumen and fecal microbiomes during the peripartum period.

RESULTS: In a longitudinal study of 91 peripartum cows, we analyzed rumen and fecal microbiomes via 16S rRNA and metagenomic sequencing across six time points. By using enterotype classification, ecological model, and random forest analysis, we identified distinct deterministic succession patterns in the rumen and fecal microbiomes (rumen: rapid transition-transition-stable; hindgut: stable-transition-stable). Key microbes, such as Succiniclasticum and Bifidobacterium, were found to drive microbial succession by balancing stochastic and deterministic processes. Notably, we observed that changes in gut microbiota succession patterns significantly influenced metabolic phenotypes (e.g., serum non-esterified fatty acid, glucose, and insulin levels). Mediation analysis suggested that specific gut microbes (e.g., Prevotella sp900315525 in the rumen and Alistipes sp015059845 in the hindgut) and metabolic pathways (e.g., glucose-related pathway) were associated with host metabolic phenotypes.

CONCLUSIONS: Overall, utilizing a large gut microbiome dataset and enterotype- and ecological model-based microbiome analyses, we comprehensively elucidated the succession and assembly of the gut microbiota in peripartum dairy cows. We further confirmed that changes in gut microbiota succession patterns were significantly related to the metabolic phenotypes of peripartum dairy cows. These findings provide valuable insights for developing health management strategies for peripartum ruminants.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Feces/microbiology
*Gastrointestinal Microbiome
Female
*Peripartum Period/metabolism
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Pregnancy

@article {pmid40388258,
year = {2025},
author = {Ebadpour, N and Abavisani, M and Sahebkar, A},
title = {Microbiome-driven precision medicine: Advancing drug development with pharmacomicrobiomics.},
journal = {Journal of drug targeting},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/1061186X.2025.2509283},
pmid = {40388258},
issn = {1029-2330},
abstract = {Pharmacomicrobiomics investigates the complicated relationship between the gut microbiome and medications, highlighting how the microbiome affects drug absorption, metabolism, and overall treatment outcomes. The interaction between pharmaceutical agents and the host microbiota is inherently bidirectional and complex. While the administration of various drugs can alter the composition and diversity of the gut microbial community, the intestinal microbiota, in turn, plays a crucial role in modulating fundamental pharmacokinetic and pharmacodynamic processes, which in turn affect the efficacy and safety of drugs. Microbial communities can influence the metabolism and efficacy of many medications in two primary ways: directly and indirectly. Direct mechanisms typically entail the induction of biochemical alterations and multiple transformations directly on the drug, whereas indirect mechanisms encompass modifications in host metabolism, alterations in the gut microbial community, the synthesis of various metabolites, and interactions with the host immune system, which indirectly influence the drug's metabolism, absorption, and efficacy. For instance, microbial communities play an important part in activating prodrugs like sulfasalazine, improving the outcomes of immunotherapy, and minimizing toxicity through specific interventions. Nonetheless, barriers can also emerge from the microbial breakdown of medications, reducing their therapeutic efficacy, along with adverse reactions mediated by microbiota. Innovations like probiotics, fecal microbiota transplantation, and microbiota profiling have shown promise in enhancing these interactions. Utilizing the distinct microbiota composition of individuals, pharmacomicrobiomics offers a route to personalized, precise, and safer therapies, signaling an important evolution in drug development and clinical practice. This study aims to provide a comprehensive overview of microbiome-drug interactions, with a particular focus on the influence of gut microbiota on drug efficacy, and to highlight their potential to revolutionize precision medicine.},
}

@article {pmid40388043,
year = {2025},
author = {Tonini, L and Ahn, C},
title = {Latest Advanced Techniques for Improving Intestinal Organoids Limitations.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {40388043},
issn = {2629-3277},
support = {RS-2022-NR074155//National Research Foundation of Korea/ ; },
abstract = {Intestinal organoids are valuable tools across different disciplines, from a clinical aspect to the biomedical research, providing a unique perspective on the complexity of the gastrointestinal system. They are alternatives to common cell lines as they can offer insights into architectural functionality and reduce the use of animal models. A deeper understanding of their organoid characteristics is required to harness their full potential. Despite their beneficial uses and multiple advantages, organoids have limitations that remain unaddressed. This review aims to elucidate the principal limitations of intestinal organoids, investigate structural defects such as the deficiency in a vascularized and lymphatic system, and absence of the microbiome, restrictions in mimicking the physiological gut model, including the lack of an acid-neutralizing system or a shortage of digestive enzymes, and the difficulties in their long-term maintenance and polarity accessibility. Development of innovative techniques to address these limitations will lead to improve in vivo recapitulation and pioneering further advancements in this field.},
}

@article {pmid40387954,
year = {2025},
author = {Warren, ML and Tsuji, K and Decker, LE and Kishi, M and Yang, J and Howe, AC and Fukami, T},
title = {Bacteria in Honeybee Crops Are Decoupled from Those in Floral Nectar and Bee Mouths.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {46},
pmid = {40387954},
issn = {1432-184X},
support = {1656518//National Science Foundation Graduate Research Fellowship Program/ ; },
mesh = {Bees/microbiology ; Animals ; *Plant Nectar ; *Bacteria/classification/isolation & purification/genetics ; *Flowers/microbiology ; Japan ; *Mouth/microbiology ; Seasons ; Gastrointestinal Microbiome ; },
abstract = {Bacteria in the honeybee gut are a well-recognized factor affecting bee health. However, the primary focus of this research has been the hindgut, while the crop, or honey stomach, is assumed to be dominated by environmentally acquired transient taxa that matter little to the bees. To evaluate this assumption, we examined bacterial taxa in the crop and mouth of Apis mellifera and A. cerana japonica foragers and in the nectar of Prunus mume flowers visited by the bees in the Minabe-Tanabe region of Japan. We found that in bacterial composition, the crop was distinct from both the mouth and the nectar, whereas mouth and nectar samples were indistinguishable. Furthermore, the crop remained similar in bacterial composition and diversity, while the mouth showed a sharp drop in alpha diversity and a large increase in beta diversity, from summer to winter. These results refute the conventional assumption, suggesting instead that the crop contains a conserved bacterial community largely distinct from environmental taxa. We also found that strains of a crop-associated species, Apilactobacillus kunkeei, could be season- and host species-specific. Together, these findings suggest that crop-associated bacterial communities should be studied further to better understand the relationship between honeybees and their gut bacteria.},
}

Bees/microbiology
Animals
*Plant Nectar
*Bacteria/classification/isolation & purification/genetics
*Flowers/microbiology
Japan
*Mouth/microbiology
Seasons
Gastrointestinal Microbiome

@article {pmid40387516,
year = {2025},
author = {Kochkarian, T and Nagy, HI and Li, Q},
title = {Gut-Heart Axis: Cardiac Remodeling and Heart Failure in the Context of Inflammatory Bowel Disease and Dysbiosis.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00016.2025},
pmid = {40387516},
issn = {1522-1547},
support = {R01 HL152683/HL/NHLBI NIH HHS/United States ; },
abstract = {Inflammatory bowel diseases (IBD), including Crohn's disease and ulcerative colitis, are debilitating and complex chronic gastrointestinal disorders that affect not only the gut but also extraintestinal organs, including the heart. The gut-heart crosstalk has garnered increasing attention in recent years; however, the molecular mechanisms underlying this complex interplay remain poorly understood. This review explores the gut-heart axis, focusing on how IBD disrupts gut microbiota homeostasis and promotes cardiac remodeling through systemic inflammation and various mediators, ultimately contributing to the onset or progression of heart failure. IBD compromises the integrity of the intestinal barrier, allowing microbial metabolites such as trimethylamine N-oxide and phenylacetylglutamine, along with inflammatory cytokines and microRNAs (miRNA) (e.g., miR-155, miR-21, let-7a), to enter the circulation and contribute to cardiac remodeling and heart failure. We identify dysfunction of nucleotide-binding oligomerization domain-containing protein 2 as a critical link between gut immunity and cardiovascular pathology. Additionally, we discuss emerging microbiome-based therapeutic strategies, including fecal microbiota transplantation and IL-23 inhibitors, aimed at restoring gut homeostasis and mitigating cardiovascular risk. By integrating molecular mechanisms, clinical evidence, and therapeutic approaches, this review underscores the pivotal role of gut dysbiosis in cardiac dysfunction and offers new perspectives for managing cardiac dysfunction in patients with IBD.},
}

@article {pmid40387510,
year = {2025},
author = {Kang, Z and Jiang, S and Fang, JY and Chen, H},
title = {Intestinal dysbiosis and colorectal cancer.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40387510},
issn = {2542-5641},
abstract = {Colorectal cancer (CRC) is one of the leading causes of cancer-related morbidity and mortality worldwide, highlighting the urgent need for novel preventive and therapeutic strategies. Emerging research highlights the crucial role of the gut microbiota, including bacteria, fungi, viruses, and their metabolites, in the pathogenesis of CRC. Dysbiosis, characterized by an imbalance in microbial composition, contributes to tumorigenesis through immune modulation, metabolic reprogramming, and genotoxicity. Specific bacterial species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, along with fungal agents like Candida species, have been implicated in CRC progression. Moreover, viral factors, including Epstein-Barr virus and human cytomegalovirus, are increasingly recognized for their roles in promoting inflammation and immune evasion. This review synthesizes the latest evidence on host-microbiome interactions in CRC, emphasizing microbial metabolites, such as short-chain fatty acids and bile acids, which may act as both risk factors and therapeutic agents. We further discuss the latest advances in microbiota-targeted clinical applications, including biomarker-assisted diagnosis, next-generation probiotics, and microbiome-based interventions. A deeper understanding of the role of gut microbiome in CRC pathogenesis could pave the way for diagnostic, preventive, and personalized therapeutic strategies.},
}

@article {pmid40387487,
year = {2025},
author = {Milhouse, W and Organski, AC and Sun, X and Ai, D and Zhou, B and Cross, TL and Ren, H},
title = {Microbiome affects mice metabolic homeostasis via differential regulation of gene expression in the brain and gut.},
journal = {Physiological reports},
volume = {13},
number = {10},
pages = {e70373},
doi = {10.14814/phy2.70373},
pmid = {40387487},
issn = {2051-817X},
support = {R01DK120772//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; R00DK098294//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; R03TR003350//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; UM1TR004402//HHS | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; //Indiana University School of Medicine/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Mice ; *Homeostasis ; *Brain/metabolism ; Mice, Inbred C57BL ; Leptin/blood/metabolism ; Receptors, G-Protein-Coupled/metabolism/genetics ; Germ-Free Life ; Gene Expression Regulation ; Cholecystokinin/metabolism ; },
abstract = {The gut microbiome (GMB) regulates digestion, metabolism, immunity, and energy homeostasis. This study investigates how gut microbiota integrate the regulation in the neuroendocrine and enteroendocrine systems, with a focus on G protein-coupled receptors (GPCRs) in the brain-gut axis and sex differences. Germ-free (GF) mice exhibited increased hypothalamic expression of the anorexigenic neuropeptide and decreased expression of the negative regulator of leptin signaling. GF males had significantly lower serum leptin levels compared to conventional (CON) males, highlighting a potential link between the microbiome and leptin resistance. In the gut, GF mice demonstrated heightened expression of anorexigenic gut hormones, including peptide YY (Pyy) and cholecystokinin (Cck), in addition to increased levels of G protein-coupled receptors (GPCRs) involved in gut hormone secretion and nutrient metabolism, particularly in females. While carbohydrate metabolism genes were upregulated in CON mice, lipid metabolism genes were predominantly higher in GF mice. These findings suggest that the gut microbiota downregulates genes involved in appetite suppression, modulates GPCRs linked to gut hormone secretion, and contributes to leptin resistance, particularly in males. This research underscores the importance of the gut microbiome in host metabolism and reveals potential molecular targets for novel treatments of metabolic diseases.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
Mice
*Homeostasis
*Brain/metabolism
Mice, Inbred C57BL
Leptin/blood/metabolism
Receptors, G-Protein-Coupled/metabolism/genetics
Germ-Free Life
Gene Expression Regulation
Cholecystokinin/metabolism

@article {pmid40387449,
year = {2025},
author = {Rose, AE and Fansler, RT and Zhu, W},
title = {Commensal resilience: ancient ecological lessons for the modern microbiota.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0050224},
doi = {10.1128/iai.00502-24},
pmid = {40387449},
issn = {1098-5522},
abstract = {The gut microbiota constitutes a complex ecosystem essential for host health, offering metabolic support, modulating the immune system, and protecting against pathogens. However, this community faces constant destabilizing challenges, including dietary changes, antibiotics, and enteric infection. Prolonged microbiota imbalance or dysbiosis can exacerbate intestinal disease states, including inflammatory bowel disease and colorectal cancer. Understanding the mechanisms that sustain microbiota resilience in the face of these imbalances is crucial for maintaining host health and developing effective therapeutics. This review explores microbiota resilience through the lens of an ecological model, emphasizing the interplay between microbial communities and host-driven environmental controls. We highlight two critical factors shaping microbiota resilience: oxygen tension and iron availability-challenges encountered by ancient anaerobic organisms during early evolutionary history, from which the predominant members of the microbiota have descended. Disruptions in intestinal anaerobiosis during inflammation increase luminal oxygen levels, favoring pro-inflammatory facultative anaerobes and depleting obligately anaerobic commensals. Simultaneously, host nutritional immunity restricts iron availability, further challenging commensal survival. This dual environmental challenge of rising oxygen tension and reduced iron availability is a convergent outcome of a diverse array of perturbations, from pathogen invasion to antibiotic treatment. By highlighting these conserved downstream environmental challenges rather than the specific upstream perturbations, this ecological view offers a focused framework for understanding microbiota resilience. This perspective not only enhances our understanding of host-microbiota interactions but also informs therapeutic strategies to foster resilience and support host health.},
}

@article {pmid40387412,
year = {2025},
author = {Holdsworth, EA and Williams, JE and Pace, RM and Caffé, B and Gartstein, M and McGuire, MA and McGuire, MK and Meehan, CL},
title = {Postpartum Maternal Stress is Unrelated to the Infant Fecal Microbiome, but is Associated With the Human Milk Microbiome in Exclusively Breastfeeding Mother-Infant Dyads: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES).},
journal = {American journal of human biology : the official journal of the Human Biology Council},
volume = {37},
number = {5},
pages = {e70061},
doi = {10.1002/ajhb.70061},
pmid = {40387412},
issn = {1520-6300},
support = {//Health Equity Research Center, Washington State University/ ; /GM/NIGMS NIH HHS/United States ; //National Institute of Food and Agriculture/ ; //Medela/ ; },
mesh = {Humans ; *Breast Feeding/statistics & numerical data ; *Feces/microbiology ; Female ; *Milk, Human/microbiology ; Adult ; *Gastrointestinal Microbiome ; Infant ; *Postpartum Period/psychology ; *Stress, Psychological ; *Mothers/psychology ; Male ; Young Adult ; Infant, Newborn ; },
abstract = {OBJECTIVES: This study aimed to evaluate whether postpartum maternal stress is associated with infant gastrointestinal microbiome composition and diversity, and whether this relationship may be mediated by maternal caregiving and breastfeeding behaviors and human milk microbiome (HMM) composition.

METHODS: Infant fecal and human milk samples were collected from 51 exclusively breastfeeding mother-infant dyads in the Pacific Northwest between 1 and 6 months postpartum. Infant fecal samples with sequencing read counts > 773 (n = 48) and milk samples with read counts > 200 (n = 46) were analyzed for bacterial alpha diversity (richness, Shannon diversity), beta diversity (Bray-Curtis dissimilarity), and genera differential abundances. Infant fecal microbiome (IFM) measures were tested for associations with mothers' self-reported Parenting Stress Index total and subscale scores in regression (richness, Shannon diversity), envfit (beta diversity), and MaAsLin2 (genera abundance) models. Potential mediators of the relationship between maternal stress and IFM were explored (observed total time breastfeeding; maternal-infant physical contact frequency; and HMM alpha diversity, beta diversity, and genera abundance).

RESULTS: Maternal stress was not associated with IFM alpha or beta diversities. Two maternal stress subscales were associated with differential abundances of Erysipelotrichaceae UCG-003 (positively) and Eggerthella (negatively) in infant feces. Maternal total stress and two stress subscales (Role Restriction, Attachment) were associated positively with HMM beta diversity (qattachment = 0.07) and negatively with HMM richness (qtotal = 0.08, qrole = 0.03).

CONCLUSIONS: Postpartum stress is not consistently associated with IFM composition during exclusive breastfeeding. However, postpartum maternal stress is associated with HMM diversity, suggesting that maternal stress might influence other developmental pathways in the breastfeeding infant.},
}

Humans
*Breast Feeding/statistics & numerical data
*Feces/microbiology
Female
*Milk, Human/microbiology
Adult
*Gastrointestinal Microbiome
Infant
*Postpartum Period/psychology
*Stress, Psychological
*Mothers/psychology
Male
Young Adult
Infant, Newborn

@article {pmid40387401,
year = {2025},
author = {Sun, L and Gao, H and Chen, H and Ren, C and Zhang, J and Shen, Q and Zhu, L and Chen, D and Jin, L and Wang, C and Li, F and Yu, L},
title = {Cutaneous dysbiosis in girls with vulvar lichen sclerosus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0267424},
doi = {10.1128/spectrum.02674-24},
pmid = {40387401},
issn = {2165-0497},
abstract = {UNLABELLED: Vulvar lichen sclerosus (VLS) is a chronic skin condition affecting the vulva, causing significant discomfort, but its etiology in prepubertal girls remains poorly understood. VLS presents with itching, irritation, and pain. Recent studies suggest that cutaneous dysbiosis might play a role in VLS. Our study aims to investigate differences in the vulvar skin microbiota among prepubertal girls with VLS, those with labial adhesions, and healthy controls, and to explore potential microbial links to VLS. We performed a comparative analysis of 16S ribosomal RNA (rRNA) sequences from vulvar skin samples of 18 girls with VLS, 15 girls with labial adhesions, and 11 healthy girls. Microbial diversity was assessed using α diversity, β diversity, and LEfSe, and functional microbial pathways were predicted. No differences were observed in α diversity among groups. However, β diversity analysis revealed significant differences in microbial composition (Jaccard, P = 0.001; unweighted UniFrac, P = 0.01). VLS patients had increased levels of Parvimonas and Fastidiosipila and differed from controls and labial adhesion cases in specific taxa. The NAD salvage pathway was notably associated with VLS. These findings suggest that cutaneous dysbiosis may contribute to VLS pathogenesis, providing insights into the microbial changes associated with the disease. Identifying microbial dysbiosis in VLS patients offers new perspectives on its pathogenesis and potential treatment strategies.

IMPORTANCE: Cutaneous dysbiosis in vulvar lichen sclerosus (VLS) may play a key role in disease pathogenesis, especially when specific microbial imbalances persist in affected patients. However, most clinical evaluations focus on symptoms rather than microbial composition, risking missed opportunities for microbiome-targeted interventions. Thus, this study highlights the importance of microbiota surveillance as a potential tool for improving the diagnosis and treatment of VLS.},
}

@article {pmid40387372,
year = {2025},
author = {Lei, Z and Zhang, H and Liu, W and Sheng, J and Zhang, H and Wang, Y and Tang, Y and Wang, H and Ding, C and Qiao, W and Zhu, Y and Yang, G and Zhang, Y and Liu, Z and Zhou, N and Hu, C and Zhao, X},
title = {Dynamic and Stable Core Microbiota Assist Plants in Enriching Selenium and Reducing Cadmium Absorption.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e00862},
doi = {10.1002/advs.202500862},
pmid = {40387372},
issn = {2198-3844},
support = {2023YFD1900904//National Key Research and Development Program of China/ ; SKLEG2024225//State Key Laboratory of Environmental Geochemical/ ; 23567601H//State Key Laboratory of North China Crop Improvement and Regulation, S&T Program of Hebei/ ; 24XJTRZW13//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; WY22B04//Wuhan Municipal Health Commission/ ; Grants KJ2025-5//2025 Science and Technology Project of Hubei Geological Bureau/ ; Grants 2023AFD215//Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China/ ; D20234501//Science and Technology Research Project of Hubei Province/ ; 23xjz05R//Hubei Polytechnic University/ ; },
abstract = {Rhizosphere microbiome is crucial for regulating rhizosphere complex nutrient dynamics. However, mechanisms by which plants regulate rhizosphere microbes to manage nutrient availability under coexisting beneficial and harmful elements remain unclear. This study focuses on the rhizosphere microbiome of Brassica napus in different naturally selenium (Se)-cadmium (Cd)-rich soils, the functionality of this rhizosphere, and the changes in the availability of rhizosphere nutrients. Microbiome analysis, metagenomics, genomic analysis, strain isolation, and functional validation are performed to investigate these relationships. Results show that a significant negative correlation is observed between the rhizosphere available Se and Cd content across the plant whole growth cycle and identified a group of core microbiota that are highly positively correlated with available Se and negatively correlated with available Cd. Genomics and metagenomics analyses reveal that the core microbiota has a higher substrate preference for amino acids related to the glutathione metabolic pathway. Key glutathione-related-amino acids and synthetic microbial community significantly improve the expression of glutathione anabolism and related amino acid transport genes and enhance Se uptake and reduce Cd absorption in plants grown in various Se-Cd-rich soils. This study provides insights into the mechanisms of root-associated microbes responding to complex soil nutrients during plant growth.},
}

@article {pmid40387216,
year = {2025},
author = {Steriade, C and Thomas, SC and Xu, F and Ahituv, A and Hanin, A and Pleshkevich, M and Hwang, S and Ramirez, A and Foreman, B and Yoo, J and Eka, O and Kellogg, M and Oliger, A and Wainwright, MS and Morales, M and Gaspard, N and Hirsch, LJ and Devinsky, O and Saxena, D},
title = {Patients with status epilepticus and new-onset refractory status epilepticus display drastically altered fecal microbiomes compared to chronic epilepsy patients.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18450},
pmid = {40387216},
issn = {1528-1167},
support = {//NORSE Institute, the Daniel Raymond Wong Memorial Research Fund and CCEMRC/ ; //Parekh Center for Interdiscplinary Neurology/ ; //National Organization for Rare Disorders and American Epilepsy Society/ ; },
abstract = {OBJECTIVE: New-onset refractory status epilepticus (NORSE) occurs in people without pre-existing epilepsy or a rapidly identified structural, toxic, metabolic, or other cause. NORSE is a rare disorder with high morbidity and mortality rates and limited evidence for effective therapies. We aimed to assess whether the gut microbiome of NORSE and status epilepticus (SE) differs from that of chronic epilepsy, whether NORSE differs from SE at different disease time points, and to examine the correlations between specific gut microbiota and cytokines in NORSE and SE.

METHODS: This longitudinal cohort study observed patients with NORSE (n = 15), SE (n = 17), and chronic epilepsy who were not in SE (n = 12). NORSE patients were recruited through the NORSE Consortium. Patients with NORSE and SE underwent longitudinal serial biospecimen collection. Fecal samples were subjected to whole-community shotgun metagenomics to characterize microbiome features. Cohorts were evaluated for prokaryotic, eukaryotic, and functional diversity. Correlations between blood inflammatory cytokine levels and microbiome features and covariate analysis with critical illness and clinical treatments were examined for NORSE and SE patients during and after SE resolution.

RESULTS: During SE, NORSE and SE patients had significantly different prokaryotic, eukaryotic, and functional microbiome levels compared to chronic epilepsy patients without SE. Limited microbiome differences were observed within and between NORSE and SE, although these groups displayed differing correlation patterns between microbial species and cytokines. Patients who later died or were tube-fed harbored significantly different microbiomes than those who survived or were orally fed.

SIGNIFICANCE: NORSE and SE patients present with a more variable and dramatically different fecal microbiome than chronic epilepsy patients, which may indicate gut dysbiosis that may be reciprocally linked to inflammatory responses. Although NORSE and SE patients had similar microbiome structures, fungal and bacterial correlates with inflammatory cytokines differed between NORSE and SE, with confounding factors influencing microbiome structure. Our data suggest a microbiome-specific response to NORSE and SE, with implications for future treatment strategies.},
}

@article {pmid40386438,
year = {2025},
author = {Anton, L and Cristancho, AG and Ferguson, B and Ravel, J and Elovitz, MA},
title = {Cervicovaginal microbiome alters transcriptomic and epigenomic signatures across cervicovaginal epithelial barriers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6171614/v1},
pmid = {40386438},
issn = {2693-5015},
abstract = {Background The cervicovaginal microbiome plays a critical role in women's health, with microbial communities dominated by Lactobacillus species considered optimal. In contrast, the depletion of lactobacilli and the presence of a diverse array of strict and facultative anaerobes, such as Gardnerella vaginalis , have been linked with adverse reproductive outcomes. Despite these associations, the molecular mechanisms by which host-microbial interactions modulate cervical and vaginal epithelial function remains poorly understood. Results In this study, we used RNA sequencing to characterize the transcriptional response of cervicovaginal epithelial cells exposed to the culture supernatants of common vaginal bacteria. Our findings revealed that G. vaginalis culture supernatants upregulate genes associated with an activated innate immune response and increased cell death. Conversely, Lactobacillus crispatus culture supernatants induced transcriptional changes indicative of epigenomic modeling in ectocervical epithelial cells. Epigenomic modification by L. crispatus , was confirmed by ATAC-sequencing, which demonstrated reduced chromatin accessibility. Conclusions These results provide new insights into host-microbe interactions within the lower reproductive tract and suggests that modulating the vaginal microbiome could offer innovative therapeutic strategies to improve reproductive health.},
}

@article {pmid40386394,
year = {2025},
author = {Chiu, CJ and Chiu, E and Chang, ML},
title = {Interaction between Infection of Porphyromonas gingivalis, A Keystone Microbe of Oral Microbiome, and Serum Levels of Lutein/Zeaxanthin Is Associated with Risk for Age-related Macular Degeneration.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-6188207/v1},
pmid = {40386394},
issn = {2693-5015},
abstract = {Porphyromonas gingivalis (P. gingivalis) functions as a catalyst bacterium in the development of periodontitis, and the serum antibody level against P. gingivalis is considered a surrogate marker for the activity level of periodontopathic microbiome. The chronic systemic inflammation induced by P. gingivalis elevates the risk of various systemic and neurodegenerative disorders, including atherosclerosis, diabetes, and Alzheimer's disease. Although the connection between human microbiome and age-related macular degeneration (AMD) remains relatively unexplored, it is noteworthy that AMD shares risk factors and etiological mechanisms with diseases related to P. gingivalis . To investigate the potential association between periodontopathic microbiome and AMD occurrence, we conducted a candidate microbe approach case-control study. Our hypothesis was tested by examining the correlation between serum P. gingivalis immunoglobulin G (IgG) levels and AMD. Comparing the lowest IgG category (≤ 57 enzyme-linked immunosorbent assay units (EU)) with higher categories revealed escalating risks: the second higher category (58-65 EU) conferred almost a 30% increased risk (odds ratio (OR) = 1.28, 95% confidence interval (CI): 1.17 to 1.4), the third higher category (66-119 EU) conferred nearly a 60% increase (OR = 1.58, 95% CI: 1.46 to 1.72), and the highest category (> 119 EU) conveyed over a two-fold risk (OR = 2.04, 95% CI: 1.62 to 2.58) of early AMD. Aligning with the notion that the microbiome composition is significantly shaped by the host's diet, our analysis indicates that sustaining elevated serum levels of lutein/zeaxanthin (≥ 0.35 µmol/L or ≥ 20 µg/dL) might potentially mitigate the P. gingivalis -related AMD risk by as much as 35% (P for interaction < 0.0001). Although the precise mechanism requires additional exploration, these findings suggest a connection between nutrition and oral microbiome, emphasizing their collective role in maintaining eye health.},
}

@article {pmid40385535,
year = {2025},
author = {Marsh, SR and Beard, CE and Gourdie, RG},
title = {Milk extracellular vesicles: A burgeoning new presence in nutraceuticals and drug delivery.},
journal = {Bioengineering & translational medicine},
volume = {10},
number = {3},
pages = {e10756},
pmid = {40385535},
issn = {2380-6761},
abstract = {Mammalian milk, a multifaceted developmental biofluid, has attracted new attention due to its diverse constituents and their implications for health and disease. Among these constituents, extracellular vesicles (EVs) have emerged as focal points of investigation. EVs, including exosomes and small EVs, have demonstrated biological activity in preclinical studies-including reports of enhancement of cognition and neural complexity, promotion of gastrointestinal development, barrier function and microbiome richness, the bolstering of immune response, and facilitation of musculoskeletal maturation in neonates. The richness of milk as a source of EVs is noteworthy, with hundreds of milliliters (at >10[12] EVs/mL) of nanovesicles extractable from a single liter of milk (>10[14] EVs/starting liter of milk). Techniques such as tangential flow filtration hold promise for scalable production, potentially extending to thousands of liters. Together with the scale and increasing sophistication of the dairy industry, the abundance of EVs in milk underscores their commercial potential in various nutraceutical applications. Beyond natural bioactivity, milk EVs (mEVs) present intriguing possibilities as orally deliverable, non-immunogenic pharmaceutical carriers, with burgeoning interest in their utilization for heart disease and cancer chemotherapy and as vectors for gene-editing modules such as CrispR. This review synthesizes current knowledge on mEV biogenesis, characterization, isolation methodologies, and cargo contents. Moreover, it delves into the therapeutic potential of mEVs, both as inherently bioactive nanovesicles and as versatile platforms for drug delivery. As efforts progress toward large-scale implementation, rigorous attention to safe, industrial-scale production and robust assay development will be pivotal in harnessing the translational promise of small EVs from milk.},
}

@article {pmid40385516,
year = {2025},
author = {Reygagne, PE and Deloche-Bensmaine, C and Leclerc-Mercier, S and Faure, J and Kovylkina, N and Clavaud, C and Gueniche, A and Barbosa, V},
title = {A Selenium Disulfide-Based Shampoo Is Beneficial for Dandruff Management and Rebalancing the Scalp Microbiome of Subjects of Any Hair Type.},
journal = {Skin appendage disorders},
volume = {},
number = {},
pages = {1-12},
pmid = {40385516},
issn = {2296-9195},
abstract = {INTRODUCTION: Dandruff is a chronic scalp condition occurring in all hair types. Selenium disulfide (SeS2) shampoo is beneficial in dandruff and rebalances the scalp microbiome. However, data regarding subjects with curly hair are missing. This study assessed the clinical and scalp microbiome benefits of SeS2 shampoo in subjects of any hair type with moderate-to-severe dandruff.

METHODS: A 6-week study in adult subjects of any De La Mettrie hair type (I-VIII) assessed total dandruff, SD severity score (SSSD), erythema, hair greasiness, quality of life, discomfort, local tolerance, perceived benefit, acceptability, cosmeticity, and changes in the scalp microbiota. SeS2 shampoo was applied twice every week.

RESULTS: Overall, 93 subjects of any hair type (women: 83%, hair types: I-III: 41%, IV-V: 29%, VI-VIII: 30%) were recruited. 69% were of European and 31% of African origin. SSSD and total dandruff scores were the highest in hair type IV-V, erythema scores in hair type I-III, and the itching score in hair type VI-VIII, with no differences between hair types for any parameter. After 4 weeks, clinical signs and subject assessments had significantly (all p < 0.05) decreased in all phototypes. SeS2 shampoo significantly (p < 0.001) rebalanced the scalp microbiome. All subjects highly appreciated its benefit, acceptability, and cosmeticity. SeS2 shampoo was well tolerated.

CONCLUSION: SeS2 shampoo is beneficial in moderate-to-severe dandruff and rebalances the scalp microbiota in all hair types. SeS2 shampoo was highly appreciated by the subjects for its benefit, acceptability, and cosmeticity, allowing a potential improvement of compliance, including in the long term.},
}

@article {pmid40385447,
year = {2025},
author = {Elnaggar, JH and Lammons, JW and Ardizzone, CM and Aaron, KJ and Jacobs, C and Graves, KJ and George, SD and Luo, M and Tamhane, A and Łaniewski, P and Quayle, AJ and Herbst-Kralovetz, MM and Cerca, N and Muzny, CA and Taylor, CM},
title = {Predicting Bacterial Vaginosis Development using Artificial Neural Networks.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.02.25326872},
pmid = {40385447},
abstract = {UNLABELLED: Bacterial vaginosis (BV) is a dysbiosis of the vaginal microbiome, characterized by the depletion of protective Lactobacillus spp. and overgrowth of anaerobes. Artificial neural network (ANN) modeling of vaginal microbial communities offers an opportunity for early detection of incident BV (iBV). 16S rRNA gene sequencing and quantitative PCR was performed on longitudinal vaginal specimens collected from participants within 14 days of iBV or from healthy participants to calculate the inferred absolute abundance (IAA) of vaginal bacterial taxa. ANNs were trained using the IAA of vaginal taxa from 420 vaginal specimens to classify individual vaginal specimens as either pre-iBV (collected before iBV onset) or Healthy. Feature importance was assessed to understand how specific vaginal micro-organisms contributed to model predictions. ANN modeling accurately classified >97% of specimens as either pre-iBV or Healthy (sensitivity >96%, specificity >98%) using IAA of 20 vaginal taxa. Model prediction accuracy was maintained when training models using only a few key vaginal taxa. Models trained using only the top five most important features achieved an accuracy of >97%, sensitivity >92%, and specificity >99%. Model predictive accuracy was further improved by training models on specimens from white and black participants separately; using only three feature models achieved an accuracy >96%, sensitivity >91%, and specificity >91%. Feature analysis found that Lactobacillus species L. gasseri and L. jensenii differed in how they contributed to model predictions in models trained with data stratified by race. A total of 420 vaginal specimens were analyzed, providing a robust dataset for model training and validation.

IMPORTANCE: Bacterial vaginosis (BV) is the most common vaginal infection and is associated with numerous comorbidities. BV is associated with infertility, preterm birth, pelvic inflammatory disease, and increased risk of HIV/STI acquisition. BV is difficult to detect prior to onset, and infection commonly recurs after treatment. Our model allows for the accurate early detection of iBV by surveying the vaginal microbiome, potentially serving as a valuable tool to determine which patients are at risk of developing iBV. Early detection of iBV could lead to wider adoption of clinical interventions useful in the prevention of iBV such as live biotherapeutics, prophylactic antibiotics, and/or behavioral modifications. Our findings indicate that few microbial targets are required for accurate predictions, facilitating cost and time effective clinical testing. Similarly, our study highlights the value of developing models personalized to specific patient populations, improving accuracy while reducing the number of taxa required for accurate predictions.},
}

@article {pmid40385307,
year = {2025},
author = {McLaren, GC and Farrell, MV and Shikuma, NJ and Tran, C},
title = {Photosynthetic dependence and filament production in physical bacterial-Symbiodiniaceae interactions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf070},
pmid = {40385307},
issn = {2730-6151},
abstract = {The cnidarian microbiome consists of a wide variety of beneficial microbes that play vital roles in maintaining and fortifying host health. Photosynthesis from symbiotic dinoflagellates (in the family Symbiodiniaceae) is crucial for their symbiosis establishment with the cnidarian host. Although more is known regarding interactions between the host and its associated bacteria and dinoflagellates, there has been little investigation into the relationship between the two microbes themselves and whether photosynthesis plays a role. Through two different methods of photosynthetic inhibition of dinoflagellates (incubation in the dark or pre-treatment with a photosystem II inhibitor), we investigated how pathogenic versus beneficial bacteria physically interact with three Symbiodiniaceae strains (symbiotic and free-living). The beneficial bacterium Tritonibacter mobilis appears to interact with photosynthesizing algae only. In the absence of photosynthesis, little to no physical interactions were observed between Symbiodiniaceae and T. mobilis. Bacterial congregation around individual dinoflagellate cells was significantly lower when photosynthesis was impaired, suggesting photosynthesis is a key facilitator of interactions between T. mobilis and all three Symbiodiniaceae strains. We also investigated whether photosynthesis affects interactions between Symbiodiniaceae and the pathogen Vibrio alginolyticus. Although no discernable impacts of photosynthetic inhibition were observed with the pathogen, scanning electron microscopy uncovered various mechanisms of interaction between Symbiodiniaceae and both bacteria, one of which includes the production of filaments not previously described. Overall, our research highlights the importance of photosynthesis in initiating interactions between bacteria and both free-living and symbiotic dinoflagellates, and opens a door to new questions regarding cell-surface interactions among individual microbes.},
}

@article {pmid40384785,
year = {2025},
author = {Rivera, I and Harlow, K and Cole, RN and O'Meally, R and Garrett, W and Xiong, W and Oliver, W and Wells, JE and Summers, KL and Chhetri, N and Postnikova, O and Rempel, L and Crouse, M and Neville, B and Davies, CP},
title = {A metaproteomic analysis of the piglet fecal microbiome across the weaning transition.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1504433},
pmid = {40384785},
issn = {1664-302X},
abstract = {Microbiome analysis has relied largely on metagenomics to characterize microbial populations and predict their functions. Here, we used a metaproteomic analysis of the fecal microbiome in piglets before and after weaning to compare protein abundances as they pertain to microbial populations specific to either a milk- or plant-based diet. Fecal samples were collected from six piglets on the day of weaning and 4 weeks after transitioning to a standard nursery diet. Using the 12,554 protein groups identified in samples, we confirmed the shift in protein composition that takes place in response to the microbial succession following weaning and demonstrated the redundancy in metabolic processes between taxa. We identified taxa with roles as primary degraders based on corresponding proteins synthesized, thereby providing evidence for cross-feeding. Proteins associated with the breakdown of milk-specific carbohydrates were common among pre-weaned pigs, whereas the proteome of post-weaned piglets contained a greater abundance of proteins involved in the breaking down plant-specific carbohydrates. Furthermore, output revealed that production of propionate takes place via the propionaldehyde pathway in pre-weaned piglets, but changes to production via the succinate pathway in post-weaned piglets. Finally, a disproportionate quantity of carbohydrate-active enzymes (CAZymes) (~8%) were produced by fungi, which typically only represent ~0.1% of the microbiome taxa. Information gathered through this characterization of the metaproteome before and after weaning revealed important differences regarding the role of members in the microbial community, thereby providing information for the optimization of diets and products for both piglet and microbiome health.},
}

@article {pmid40384779,
year = {2025},
author = {Sunthornthummas, S and Wasitthankasem, R and Phokhaphan, P and Sudtachat, N and Wilantho, A and Ngamphiw, C and Chareanchim, W and Tongsima, S},
title = {Unveiling the impact of 16S rRNA gene intergenomic variation on primer design and gut microbiome profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573920},
pmid = {40384779},
issn = {1664-302X},
abstract = {The 16S rRNA gene is crucial for bacterial identification, but primer biases and intergenomic variation can compromise its effectiveness, especially in complex ecosystems like the human gut microbiome. This study systematically evaluates 57 commonly used 16S rRNA primer sets through in silico PCR simulations against the SILVA database. We identified three promising primer sets (V3_P3, V3_P7, and V4_P10) that offer balanced coverage and specificity across 20 key genera of the core gut microbiome. Our findings reveal: (1) significant limitations in widely used "universal" primers, often failing to capture microbial diversity due to unexpected variability in conserved regions, (2) substantial intergenomic variation, even within traditionally conserved regions of the 16S rRNA gene, as demonstrated by Shannon entropy analysis, and (3) discrepancies between intergenomic patterns in NCBI and SILVA databases, highlighting the impact of database choices on taxonomic classification. These results challenge assumptions about 16S rRNA gene conservation and emphasize the need for tailored primer design informed by comprehensive sequence databases. We advocate for a multi-primer strategy to improve coverage and mitigate biases, ultimately enhancing the accuracy and reliability of gut microbiome profiling. This approach has potential applications beyond gut microbiome studies, including animal microbiome research and probiotic community profiling.},
}

@article {pmid40384260,
year = {2025},
author = {Mihatsch, W and Dinleyici, EC and Canani, RB and Hojsak, I and Mosca, A and Orel, R and Salvatore, S and Savino, F and Szajewska, H and van den Akker, CHP and Weizman, Z and Vandenplas, Y and , },
title = {Technical review by the ESPGHAN Special Interest Group on Gut Microbiota and Modifications on the health outcomes of infant formula supplemented with prebiotics.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70064},
pmid = {40384260},
issn = {1536-4801},
support = {//None/ ; },
abstract = {Prebiotics are defined as substrates that are selectively utilized by host microorganisms, conferring health benefits. This technical review focusing on prebiotic-supplemented infant formulas is one of the five manuscripts developed by the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition Special Interest Group on Gut Microbiota and Modifications (SIG-GMM). The SIG-GMM conducted a technical review to evaluate the clinical outcomes of prebiotic-supplemented infant formulas in healthy infants (0-12 months) that were published before 2024. The review focused on the following clinical outcomes: anthropometric measurements, stool frequency and consistency, gastrointestinal symptoms, allergy prevention, infection prevention, and safety/tolerability. Following the review, all 20 SIG members anonymously voted on each statement, scoring them from 0 to 9. A score ≥6 indicated agreement with a statement. A statement was rejected if ≥75% of the members voted <6. Fifty-one publications were included, focusing on prebiotics such as short-chain galacto-oligosaccharides, long-chain fructo-oligosaccharides, acidic oligosaccharides, and polydextrose/galacto-oligosaccharides. This technical review demonstrates that prebiotic-supplemented formulas are well tolerated, with no significant differences in anthropometric parameters compared to those fed non-supplemented formula. Prebiotic supplementation decreased stool consistency and increased stool frequency depending on the dosage and type. This technical review provides information on prebiotic-supplemented infant formulas in healthy infants. Overall, no significant clinical health benefits were observed in terms of infections and antibiotic use, colic, and allergy.},
}

@article {pmid40384122,
year = {2025},
author = {Roca, C and Mirmozaffari, Y and Martin, WJ and Capps, N and Sullivan, KM and Thorp, BD and Ferkol, TW and Davis, SD and Kimple, A and Wolfgang, MC},
title = {Advances in Sinonasal Microbiome Analysis.},
journal = {Ear, nose, & throat journal},
volume = {},
number = {},
pages = {1455613251341711},
doi = {10.1177/01455613251341711},
pmid = {40384122},
issn = {1942-7522},
}

@article {pmid40384043,
year = {2025},
author = {Bankah, AZ and Tagoe, TA and Darko, E and Agoha, R and Ametefe, EN and Kukuia, KKE and Adjei, S},
title = {Combined Administration of Lactobacillus or Bifidobacterium Offers Enhanced Antidepressant and Anxiolytic Activity in a Dose Dependent Manner.},
journal = {Brain and behavior},
volume = {15},
number = {5},
pages = {e70564},
doi = {10.1002/brb3.70564},
pmid = {40384043},
issn = {2162-3279},
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; Male ; Mice ; *Depression/drug therapy/therapy ; *Anxiety/drug therapy/therapy ; Mice, Inbred ICR ; *Bifidobacterium ; Disease Models, Animal ; *Lactobacillus ; *Antidepressive Agents/pharmacology/administration & dosage ; Stress, Psychological ; Behavior, Animal/drug effects ; *Anti-Anxiety Agents/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; Fluoxetine/pharmacology ; },
abstract = {PURPOSE: Gut microbiota is strongly linked to the activity of the bidirectional gut-brain axis, which influences neuropsychological processes at multiple levels. Changes in the gut microbiota have been implicated in mood disorders, and probiotics have been explored for their ability to mitigate the effects of stress on mental health. Here, we investigated the therapeutic benefits of different concentrations and combinations of Lactobacillus and Bifidobacterium in a mouse model of stress induced depression and anxiety.

METHODS: Sixty-three male ICR mice (6-8 weeks old; 20-25g) divided into nine groups were used for this study. The test groups underwent chronic unpredictable mild stress protocols for two weeks before receiving low (10[4] CFU/ml) or high (10[8] CFU/ml) doses of either monotherapy (Lactobacillus or Bifidobacterium) or a combination therapy (Lactobacillus and Bifidobacterium) for four weeks. The antidepressant, fluoxetine, served as the positive control. Measurements of weight and sucrose preference were performed at four time points in addition to a battery of behavioral tests (open field tests, forced swim test, tail suspension test, and hot plate test) at the endpoint to assess depression and anxiety-like behavior.

RESULTS: Low doses of the probiotic formulation (mono- or combined therapy) reversed weight loss but not anhedonia. In contrast, high doses of probiotic formulations (mono- or combined therapy), along with fluoxetine, were effective in reversing the weight loss and anhedonia caused by chronic unpredictable mild stress. Probiotics ameliorated stress-induced immobility as measured by both the forced swim and tail suspension tests, while also reducing anxiety-like behavior (increased peripheral activity) in the open field test. High doses of mono- or combined therapy increased curling behavior in the tail suspension test, whereas fluoxetine failed to do so.

CONCLUSION: This study indicates the species- and dose-dependent beneficial effects of probiotics on behavioral outcomes associated with depression while also reversing weight loss. Evidence suggests that probiotics and fluoxetine may exert antidepressant activity via different mechanisms.},
}

Animals
*Probiotics/administration & dosage/pharmacology
Male
Mice
*Depression/drug therapy/therapy
*Anxiety/drug therapy/therapy
Mice, Inbred ICR
*Bifidobacterium
Disease Models, Animal
*Lactobacillus
*Antidepressive Agents/pharmacology/administration & dosage
Stress, Psychological
Behavior, Animal/drug effects
*Anti-Anxiety Agents/pharmacology/administration & dosage
Gastrointestinal Microbiome/drug effects
Fluoxetine/pharmacology

@article {pmid40383993,
year = {2025},
author = {Xu, X and Su, H and Chen, J and Liu, D and Chen, A and Hu, D and Cao, J and Huang, Y},
title = {Association of the Dietary Index for Gut Microbiota With Severity, Renal Function, and Sarcopenia in Patients With Chronic Kidney Disease: A Population-Based Cross-Sectional Study.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/27697061.2025.2501977},
pmid = {40383993},
issn = {2769-707X},
abstract = {OBJECTIVE: The aim of this research was to clarify the relationship between the Dietary Index for Gut Microbiota (DI-GM) and the severity of chronic kidney disease (CKD), renal function, and the prevalence of sarcopenia in patients with CKD, as well as the role of the Systemic Immune-Inflammation Index (SII) therein.

METHOD: Using data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018, the study included 2169 participants with CKD. DI-GM was calculated on a scale of 0 to 13, with higher scores indicating a healthier gut microbiome. CKD severity was categorized by estimated glomerular filtration rate (eGFR), and sarcopenia was defined using appendicular lean mass adjusted for body mass index. Statistical analyses included weighted regression models, restricted cubic spline, subgroup analysis, and mediation analysis.

RESULTS: Higher DI-GM scores were associated with lower CKD severity (odds ratio [OR], 0.85; 95% confidence interval [CI], 0.78-0.94; p = .001), improved renal function (eGFR, β = 1.078, p = .020; serum creatinine, β = -1.548, p = .026; blood urea nitrogen, β = -0.091, p = .026), and reduced sarcopenia prevalence (OR, 0.70; 95% CI, 0.57-0.87; p = .002). SII score partially mediated the association between DI-GM score and sarcopenia in CKD, accounting for 12.11% of the effect (p < .001). No significant associations were found between DI-GM score and all-cause or cardiovascular mortality among the population with CKD.

CONCLUSIONS: Findings suggest that dietary interventions targeting gut microbiota may have benefits in managing CKD severity, improving renal function, and reducing sarcopenia risk.},
}

@article {pmid40383915,
year = {2025},
author = {Kim, YJ and Lee, J and Lee, E and Park, SJ and Kim, JH},
title = {Impact of stool transplantation and metformin on polyp reduction and inflammation in an APC Min mouse model.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00011},
pmid = {40383915},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Familial adenomatous polyposis is a hereditary condition characterized by numerous adenomatous polyps in the colon and rectum, significantly increasing colorectal cancer risk. Current management strategies, such as prophylactic colectomy, are invasive and have long-term consequences, highlighting the need for alternative therapies. This study aimed to evaluate whether stool transplantation and metformin therapy synergistically reduce polyp formation and inflammation.

METHODS: APC Min mice were divided into 4 groups: control, anti-control (antibiotic pretreatment), stool (stool transplantation), and stool+metformin. Polyp burden, bacterial abundance, inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor [TNF]-α, IL-10), and tumorigenic markers (NF-κB, Cox2, c-myc, β-catenin) were assessed using messenger RNA (mRNA) and protein analyses of intestinal tissues, along with serum and fecal microbiota evaluations.

RESULTS: Stool transplantation combined with metformin significantly reduced bacterial abundance and polyp burden. The anti-control group showed similar reductions, suggesting suppression of gut microbiota re-establishment. TNF-α and IL-10 levels remained unchanged, but a significant increase in IL-6 was observed in the stool+metformin group's intestinal tissues, indicating localized immune activation. Intestinal Cox2 mRNA expression was reduced in the combination group, correlating with polyp suppression. Protein levels of NF-κB, Cox2, and β-catenin showed no significant changes in vivo, while in vitro experiments revealed a decrease in NF-κB and an increase in Cox2, suggesting complex regulation of inflammation-related pathways.

CONCLUSIONS: Stool transplantation combined with metformin reduces polyp burden in APC Min mice through gut microbiota modulation and localized immune activation. These findings support the therapeutic potential of this combination treatment for familial adenomatous polyposis.},
}

@article {pmid40383872,
year = {2024},
author = {Gao, YZ and Wu, YM and Tang, L and Hu, XJ and Wang, J},
title = {Progress in bioremediation of organic contaminated soil based on microbiome.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {12},
pages = {3225-3234},
doi = {10.13287/j.1001-9332.202412.029},
pmid = {40383872},
issn = {1001-9332},
mesh = {Biodegradation, Environmental ; *Soil Pollutants/metabolism/isolation & purification ; *Soil Microbiology ; *Microbiota ; *Organic Chemicals/metabolism/isolation & purification ; },
abstract = {There are a variety of toxic and widely distributed organic contaminants in soils, threatening ecological safety and human health. Bioremediation technology primarily addresses soil pollutants through enzymatic reactions of microorganisms. Nevertheless, the effectiveness of bioremediation technology is much lower when treating contaminated soils with multiple organic pollutants. The combination between microbiome technology and bioremedia-tion is one of the hot topics in the research area of soil remediation. In recent years, there are rapid progresses in bioremediation research based on genomics, transcriptomics, proteomics and metabolomics. Based on technology of genomics, the composition of soil microorganisms could be analyzed, identified, eliminated, and finally functional microbiome can be screened. Consequently, functional microbiome could be constructed and targeted according to the characteristics of organic pollutants. Transcriptomics could help discover unknown functional genes, and explore new pathways for organic pollutant degradation. Proteomics and metabolomics would help improve the degradation efficiency of organic pollutants. We reviewed the challenges in bioremediation of organic-contaminated soil, analyzed microbiome methods being used in bioremediation, and examined the principles and effectiveness of microbiome-based bioremediation with empirical studies. Currently, omics technology is still at its early stage in the field of organic soil contamination bioremediation, with more crucial data being needed. Utilizing microbiome methods for molecular operations, innovating organic-contaminated soil bioremediation systems and elucidating the restoration mechanisms will be the key for efficient application of bioremediation technologies.},
}

Biodegradation, Environmental
*Soil Pollutants/metabolism/isolation & purification
*Soil Microbiology
*Microbiota
*Organic Chemicals/metabolism/isolation & purification

@article {pmid40383597,
year = {2025},
author = {Cheng, B and Feng, H and Li, C and Jia, F and Zhang, X},
title = {The mutual effect of dietary fiber and polyphenol on gut microbiota: Implications for the metabolic and microbial modulation and associated health benefits.},
journal = {Carbohydrate polymers},
volume = {358},
number = {},
pages = {123541},
doi = {10.1016/j.carbpol.2025.123541},
pmid = {40383597},
issn = {1879-1344},
mesh = {*Polyphenols/pharmacology/metabolism ; *Dietary Fiber/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fatty Acids, Volatile/metabolism ; Animals ; },
abstract = {Gut microbiota plays a critical role in maintaining human health by regulating digestion, metabolism, and immune function. Emerging research highlights the potential of dietary interventions, particularly dietary fiber (DF) and polyphenols, in modulating gut microbiota composition and function. DF serves as a fermentable substrate for beneficial gut bacteria, promoting the production of short-chain fatty acids (SCFAs). Polyphenols, a diverse group of bioactive compounds selectively modulate microbial populations and contribute to the production of bioactive metabolites with host health benefits. Importantly, the interplay between DF and polyphenols creates a synergistic effect within the gut microbiome, shaping microbial diversity, enhancing SCFAs production, and strengthening gut barrier function, which together support metabolic and immune homeostasis. This review systematically explores the synergistic effects of DF-polyphenol combinations on gut microbiota modulation, microbial metabolites, and their implications for overall health. The combined effects of DF and polyphenols hold promise for targeted nutritional strategies in preventing metabolic disorders and improving gut health. Moreover, the extent of these benefits is influenced by the structural characteristics of DF, the source and dosage of polyphenols, and individual gut microbiota composition. Further research is warranted to optimize DF-polyphenol interactions and facilitate their applications in personalized nutrition and functional food development.},
}

*Polyphenols/pharmacology/metabolism
*Dietary Fiber/pharmacology/metabolism
*Gastrointestinal Microbiome/drug effects
Humans
Fatty Acids, Volatile/metabolism
Animals

@article {pmid40383540,
year = {2025},
author = {Schoch, JJ and Anderson, KR and Jones, AE and Tollefson, MM and , },
title = {Atopic Dermatitis: Update on Skin-Directed Management: Clinical Report.},
journal = {Pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1542/peds.2025-071812},
pmid = {40383540},
issn = {1098-4275},
abstract = {Atopic dermatitis affects 20% to 25% of children and has significant impact on quality of life of patients and families. Recent studies of the pathogenesis of AD highlight the interplay between a defective skin barrier, immune dysfunction, and the cutaneous microbiome. Standard of care for AD treatment includes topical corticosteroids for active disease and moisturization to repair the barrier defect. Emerging treatments include dupilumab and Janus kinase (JAK) inhibitors. Reduction of triggers and proactive treatment with topical corticosteroids and/or topical calcineurin inhibitors can reduce flares. Treatment plans should be clear and as simple as possible to maximize adherence.},
}

@article {pmid40383487,
year = {2025},
author = {Quinn, BE and Reyes Rodríguez, JA and Sam, EK and Duliman, J and Denn, E and Lee, S and Shan, L and Kuti, C and Nyann, BI and Rosario-Matos, N and Wang, L},
title = {The nasal microbiome in early infancy is primarily shaped by the maternal nasal microbiome.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.05.004},
pmid = {40383487},
issn = {1097-6825},
abstract = {BACKGROUND: The infant nasal microbiota closely mediates the risks of developing childhood respiratory diseases. However, the primary sources of these early residing bacteria remain largely unknown, preventing the development of microbiome strategies for disease prevention.

OBJECTIVE: Identify the primary maternal source of bacteria found in the early infant nasal microbiome.

METHODS: We conducted a birth cohort study, named Mother Infant Microbiome International Cohort (MIMIC). We recruited 95 mother-newborn dyads from three sites (St. Louis, Missouri, United States; San Juan, Puerto Rico; and Accra, Ghana) and collected samples at two time points (at birth and around two months of age). We performed analyses on 16S ribosomal RNA gene sequencing data to evaluate the maternal microbiomes (nasal, saliva, breast milk, and areola skin) as sources seeding the infant nasal microbiome.

RESULTS: The infant nasal microbiome underwent a major compositional change during the first two months of life. The maternal nasal microbiome was identified as the primary source of bacteria in the early nasal microbiome across the three regions. Corynebacterium was predominantly transferred from the maternal nasal microbiome. Infants were more likely to harbor a Corynebacterium-dominant nasal microbiome if their mother's nasal microbiome was Corynebacterium-dominant.

CONCLUSIONS: The maternal nasal microbiome is an important source of bacteria in the early nasal microbiome. A large portion of transmitted bacteria from the maternal nasal microbiome was a generally beneficial bacterial genus, Corynebacterium. Results from this study will aid the development of early life intervention strategies that aim to reduce the incidence of childhood respiratory diseases and asthma.},
}

@article {pmid40383409,
year = {2025},
author = {Hu, D and Zhao, J and Wu, M and Zhou, Y and Lyu, B and Xu, C and Huang, C and Su, Z and Zhang, H and Guo, J and Tang, W and Chen, G and Li, Q},
title = {Microbial Interactions Induce the Mutational Signature of Mismatch Repair Deficiency in Colorectal Cancer and Associated with EPPK1 Mutations.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217807},
doi = {10.1016/j.canlet.2025.217807},
pmid = {40383409},
issn = {1872-7980},
abstract = {To better understand the impact of microbial interactions on the clonal evolution of colorectal cancer (CRC), we conducted high-resolution profiling of the gut microbiome of 101 treatment-naïve primary CRC patients using nanopore sequencing. We performed an integrated analysis of microbiome and tumor exome data to identify symbiotic microbes that interactively influence the mutational processes and the subsequent clonality of CRC. Our results suggested that Dialister pneumosintes and Fusobacterium animalis were both associated with somatic EPPK1 mutations and promote SBS6 (mismatch repair deficiency, dMMR) activity. Notably, we showed that the symbiotic architecture of Dialister pneumosintes and Fusobacterium animalis undergoes significant changes with the mutational status of EPPK1. In addition, we identified specific metabolic pathways involving key metabolites that potentially mediate microbial interactions in CRC. These findings provide new insights into the interplay between the gut microbiome and the mutation landscape of colorectal cancer, thereby informing the clonal evolution of CRC and new strategies for precision medicine.},
}

@article {pmid40383402,
year = {2025},
author = {Schimmele, T and Langgartner, D and Gebauer, D and Mazzari, G and Probst, J and Weingast, G and Ignatius, A and Tabacco, G and Naciu, AM and Messina, MV and Palermo, A and Reber, SO and Haffner-Luntzer, M},
title = {Early life adversity promotes a milieu in favor of catabolic bone turnover in females: Mycobacterium vaccae NCTC 11659 proofs protective in preclinical studies.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.05.009},
pmid = {40383402},
issn = {1090-2139},
abstract = {Despite early clinical studies supporting the hypothesis that early life adversity (ELA) negatively affects the bone and despite typical ELA-associated disorders, including post-traumatic stress disorder (PTSD) and major depressive disorder (MD), are associated with osteoporosis and increased bone fracture risk, preclinical studies do not support this association. However, previous studies were only performed using male and not female mice. In the current study we showed that ELA, induced by the classical maternal separation (MS) paradigm, facilitated femoral osteoclast activity specifically in female but not male mice. This was associated with a transient decline in both intestinal alpha diversity and Firmicutes/Bacteroidetes ratio, suggesting that the microbiome-gut-bone axis is involved in these effects. Moreover, ELA long-lastingly increased the femoral mRNA expression of the proinflammatory cytokine Interleukin-6 (IL-6) and the osteoclastic markers Cathepsin K and RANKL. Importantly, all sex-specific ELA effects on bone were absent in female mice administered with M. vaccae NCTC 11659 following ELA exposure. Finally, our clinical data indicate strong associations between ELA and development of an osteopenic/osteoporotic bone phenotype in postmenopausal women undergoing bone diagnostics. Together, our preclinical and clinical findings indicate that i) ELA negatively affects the bone, ii) these effects are specific for female sex, iii) the negative effects of ELA on female bone are associated with transient changes in the composition of the intestinal microbiome followed by long-lasting activation of the immune system and the HPA axis, together setting the stage for a facilitated catabolic bone turnover and development of an osteopenic/osteoporotic bone phenotype, iv) developing immunoregulatory approaches, such as repeated s.c. administrations with immunoregulatory microorganisms, have potential for prevention/treatment of ELA-related bone disorders.},
}

@article {pmid40383397,
year = {2025},
author = {Merrick, B and Prossomariti, D and Allen, E and Bisnauthsing, K and Kertanegara, M and Sergaki, C and Le Guennec, AD and Delord, M and Bell, JT and Conte, MR and Moyes, DL and Shankar-Hari, M and Douiri, A and Goodman, AL and Shawcross, DL and Goldenberg, SD},
title = {Faecal microbiota transplant to ERadicate gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO): a feasibility randomised controlled trial.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106504},
doi = {10.1016/j.jinf.2025.106504},
pmid = {40383397},
issn = {1532-2742},
abstract = {OBJECTIVES: The gastrointestinal tract (GIT) is a reservoir of multidrug-resistant organisms (MDRO). Colonisation with MDRO precedes invasive infections which can be challenging to treat with excess morbidity and mortality compared to antimicrobial susceptible infections. Currently, there are no effective GIT decolonisation strategies. Whilst Faecal Microbiota Transplant (FMT) has emerged as a potential therapeutic, there remains uncertainty about its feasibility, safety and efficacy.

METHODS: Population: Patients with invasive infection with Extended-spectrum Beta-Lactamase (ESBL-) or Carbapenem-resistant Enterobacterales (CRE) and persistent GIT carriage.

INTERVENTION: Three doses of encapsulated lyophilised FMT.

COMPARATOR: Matched placebo capsules.

OUTCOMES: Primary outcome was participant consent rate as a proportion of those approached to be screened for GIT carriage of ESBL-E/CRE. Secondary outcomes were additional feasibility, safety and tolerability, and efficacy metrics. Exploratory outcomes included stool metagenomic analysis.

RESULTS: Of 460 approached individuals, 124 (27%) consented. 53/124 participants (43%) fulfilled all eligibility criteria. 44/53 (83%) of those eligible were randomised and 41/44 (93%) received investigational medicinal product (IMP): 20 FMT and 21 placebo. 39/41 (95%) completed IMP dosing. Abdominal bloating and skin and subcutaneous tissue disorders were more common following FMT but there were no unanticipated harms. MDRO carriage decreased over time across arms but was lower at all time points in the FMT arm. FMT increased microbiome diversity and microbiome-based health measures. FMT recipients' samples clustered into two groups with those with more dissimilar community composition to donors more likely to decolonise post-FMT (3/5 vs. 0/12, p=0.01). Patients that decolonised exhibited a trend towards increased proportional representation of donor-derived strains in their post-FMT samples (p=0.05) and change in strain dominance within MDRO at species-level.

CONCLUSIONS: Progression to a substantive trial is feasible with modifications to the existing FERARO protocol. FMT was safe, well tolerated, and acceptable to patients colonised with MDRO. Microbiome analysis infers that greater donor-recipient microbiome dissimilarity at baseline and higher rates of donor-derived strain engraftment favour MDRO decolonisation, which in turn maybe facilitated by conspecific strain replacement.},
}

@article {pmid40383390,
year = {2025},
author = {Flynn, A and Barton, W and McAloon, C and McFadden, M and Crispie, F and McPherson, SE and Allendez, G and Murphy, JP and McAloon, CG and Cotter, PD and Kennedy, E},
title = {Effects of feeding a simulated waste milk on growth, health, fecal microbiota, and antibiotic resistance in dairy heifer calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26062},
pmid = {40383390},
issn = {1525-3198},
abstract = {Feeding waste milk, a common practice in dairy farming, exposes calves to subtherapeutic levels of antimicrobials, potentially contributing to antibiotic resistance-a growing concern globally. Many dairy farmers, including those in Ireland, continue this practice, feeding waste milk from antibiotic-treated cows to calves. Although previous studies have linked waste milk feeding to changes in calf growth and health during the preweaning period, its effects postweaning remain unclear. This study examined how the duration of antimicrobial exposure at levels equivalent to those found in waste milk influences health and growth outcomes of dairy heifer calves both before and after weaning. It also assessed the prevalence of extended-spectrum β-lactamase (ESBL)-resistant Escherichia coli in feces and changes in the fecal microbiota over time. To mimic waste milk, as derived from a cow treated with an intramammary suspension of antibiotics, a simulated waste milk (SWM) was prepared by adding amoxicillin (1.68 mg/L) and neomycin (2.28 mg/L) to a conventional milk replacer (MR). The study employed a randomized block design with 87 dairy heifer calves assigned to 1 of 3 treatments: (1) long-term antibiotic (LTA), with calves fed SWM until weaning at 12 wk; (2) short-term antibiotic (STA), with SWM fed from 3 to 5 wk; and (3) control (CONT), with calves fed antibiotic-free MR. Calves were weighed weekly, and health scores, including fecal scores (tail and hindquarters cleanliness as diarrhea indicator), were recorded twice per week. Fecal and blood samples were collected to analyze microbiome changes and the shedding of antimicrobial resistance. Blood samples were taken to measure systemic inflammation, using serum amyloid A as a biomarker. Results indicated that SWM feeding did not affect average daily gains before or after weaning. However, higher fecal scores were observed in the LTA group during weaning and after weaning in the STA group. Antibiotic-resistant isolates were present in all groups, with the highest prevalence in LTA. Fecal microbiota analysis revealed treatment-specific microbial community variations, with increase of Enterococcus faecium genes resistant to macrolide, aminoglycoside, and tetracycline antibiotics in LTA and STA compared with CONT. In summary, SWM feeding did not significantly affect growth or overall health, but it was associated with increased fecal shedding of resistant bacteria and some changes in the microbiota, indicating potential long-term implications for antimicrobial resistance in dairy herds.},
}

@article {pmid40383389,
year = {2025},
author = {Yu, Y and Fu, R and Jin, C and Gao, H and Han, L and Qi, M and Fu, B and Li, Q and Wang, Y and Cheng, Y and Leng, J},
title = {Ruminal microbiome-host metabolome crosstalk in the synthesis of unsaturated fatty acids in buffalo milk.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26176},
pmid = {40383389},
issn = {1525-3198},
abstract = {Interactions between rumen microorganisms and their metabolites contribute to milk yield and milk fat content in dairy cows. However, whether rumen microbes and host metabolism affect fatty acid synthesis in milk is unknown. In this study, we investigated the potential regulatory mechanisms affecting the unsaturated fatty acid content of Binglangjiang buffalo by using macrogenomics and metabolomics. Macrogenomic analysis showed that Bacteroides was significantly more abundant in the high UFA group (HF), contributing to the improvement of functions related to fatty acid synthesis. Then, we found that the rumen microbiota of the HF group was enriched in 2 important pathways involved in lipid metabolism (i.e., fatty acid biosynthesis and fatty acid metabolism), suggesting that more fatty acids were synthesized in the HF group. Metabolomics analyses showed that most of the UFA were more abundant in the HF group, which was also confirmed by the quantification of related metabolic pathways in milk fatty acids, suggesting that the HF group has a higher capacity to synthesize MUFA and PUFA. Correlation analysis of rumen lipid metabolic pathways and metabolites revealed that metabolic pathways such as fatty acid biosynthesis, fatty acid metabolism, metabolic pathways, and peroxisome proliferator-activated receptor (PPAR) signaling pathway, which were significantly enriched in the HF group compared with the low UFA group, were significantly and positively correlated with multiple UFA . The synthesis of UFA is mainly influenced by Bacteroides, Prevotella, and Bacteroidaceae, and regulated by fatty acid biosynthesis, fatty acid metabolism, and PPAR signaling pathways, which together influence the synthesis of UFA in buffaloes.},
}

@article {pmid40383313,
year = {2025},
author = {Ren, J and Ren, X and Deng, Z and Zhang, H and Wang, J and Zhang, C and Lu, F and Shi, J},
title = {Ecological effects of biochar in heavy metal-contaminated soils from multidimensional perspective: Using meta-analysis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132695},
doi = {10.1016/j.biortech.2025.132695},
pmid = {40383313},
issn = {1873-2976},
abstract = {The application of biochar in the remediation of heavy metal-contaminated soil shows great potential, but its comprehensive impacts on metal dynamics and the soil ecosystem have not been quantified. This study conducted a meta - analysis of 496 observations from 41 studies. The results indicated that biochar can significantly decrease the bioavailability of cationic metals, but has limited effect on anionic heavy metals. After application, soil nutrient content and enzyme activity significantly increased. Microbial network analysis revealed enhanced interactions between species, and the reconstruction of the core microbial community indicated a shift in microbial survival strategies from resisting heavy metal stress to nutrient cycling and plant symbiosis. FAPROTAX analysis showed that microbial communities related to nitrogen and sulfur cycles were significantly stimulated. This study explores the role of biochar in restoring soil multifunctionality while addressing metal pollution issues from multiple perspectives, offering key insights for developing targeted soil remediation strategies.},
}

@article {pmid40383300,
year = {2025},
author = {Li, Z and Wang, X and Du, H and Liu, W and Zhang, C and Talifu, Z and Xu, X and Pan, Y and Zhang, J and Ke, H and Yang, D and Gao, F and Yu, Y and Jing, Y and Li, J},
title = {Unraveling Spinal Cord Injury Nutrition: Effects of Diet on the Host and Microbiome.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100448},
doi = {10.1016/j.advnut.2025.100448},
pmid = {40383300},
issn = {2156-5376},
abstract = {Spinal cord injury (SCI) leads to severe neurological dysfunction with significant nutritional alterations. These alterations are closely associated with gut dysbiosis and neurogenic gut dysfunction after SCI, creating complex interactions that further exacerbate metabolic disturbances and impede neurological recovery. In the context of SCI, diet not only fulfills basic nutritional needs but also serves as an important therapeutic tool to modulate these interactions. This review provides a broad overview of existing research findings, analyzes the impact of existing dietary interventions on SCI, and attempts to clarify the complex relationship between diet and host and gut microbiota. We hope to provide a clear direction for future research and a scientific basis for the development of personalized dietary interventions to improve the nutritional status of SCI patients, reduce the incidence of complications such as metabolic disorders, and promote the recovery of neurological function and overall quality of life of SCI patients. STATEMENT OF SIGNIFICANCE: This review evaluates the nutritional changes in patients with spinal cord injury, comprehensively elucidating the effects of dietary interventions on SCI patients from both the host and gut microbiota perspectives. By revealing the complex interactions among them, it lays the foundation for developing personalized nutritional intervention strategies to optimize recovery and improve long-term health outcomes in the future.},
}

@article {pmid40383241,
year = {2025},
author = {Chen, YM and Yeh, CA and Lin, WH and Lin, CN and Chiou, MT},
title = {Dynamic Alterations of the Intestinal Microbiome and Metabolome During Transmissible Gastroenteritis Virus Infection in Weaned Pigs.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107705},
doi = {10.1016/j.micpath.2025.107705},
pmid = {40383241},
issn = {1096-1208},
abstract = {Transmissible gastroenteritis virus (TGEV) infection induces diarrhea in piglets by targeting the small intestine, especially the jejunum and ileum. However, dynamic changes in the gut microbiota and metabolome during TGEV infection remain unclear. This study investigated these alterations and their association with intestinal damage in weaned pigs during early TGEV infection. Thirty 4-week-old pigs were allocated randomly into TGEV-inoculated and mock groups. On days 3, 5, and 7 postinoculation, intestinal tissue and fecal samples were collected. Full-length 16S rRNA sequencing and ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC‒MS/MS) were employed to analyze microbiota composition and nontargeted metabolites. TGEV infection resulted in reduced villous height-to-crypt depth (VH:CD) ratios (P < 0.01) and significantly altered microbial diversity (P = 0.0091 in jejunum) and composition (P = 0.001). Notably, infected pigs showed increased abundances of Lactobacillus and Limosilactobacillus species. The VH:CD ratio correlated with the overall taxonomic composition in both the jejunum and ileum (r = 0.4, P < 0.001) and was positively associated with microbial functions such as aerobic chemoheterotrophy and chitinolysis in the jejunum. Fecal metabolomics revealed 1,815 and 892 differentially expressed metabolites in the jejunum and ileum, respectively, including amino acids, fatty acids, and intermediates of energy metabolism. Integrated analysis revealed that Lactobacillus amylovorus DSM20531 was positively correlated with linoleic acid, L-tyrosine, and citric acid, whereas Lactococcus lactis showed a negative correlation with isocitric acid and glutamine. This study enhances our understanding of the pathogenesis of TGEV and provides potential microbial and metabolic biomarkers for future diagnostic and preventive strategies.},
}

@article {pmid40382931,
year = {2025},
author = {Subedi, SC and Epps, S and Ankrah, N and Bhandari, S},
title = {Soil microbes' role in plant germination and growth under salt stress.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125841},
doi = {10.1016/j.jenvman.2025.125841},
pmid = {40382931},
issn = {1095-8630},
abstract = {One significant consequence of climate change is the rising sea levels, which contribute to the intrusion of saltwater towards the inland and groundwater placing extreme salt stress on many plants. Beneficial interactions with microorganisms may be crucial for ameliorating salt stress and facilitating the ecosystem services plants provide. We aimed to test if microbes aid plants in coping with salinity stress and to identify potential applications for enhancing plant resilience in the face of ongoing environmental changes. We set up a factorial experiment that manipulated the introduction of field collected soil microbes, the salinity of these introduced microbes, and the salinity of the water in which plants were grown (freshwater vs. saltwater). To identify the impact of native microbes on the survival of plants in high stress environments, specifically we examined how a Liatris spicata, a freshwater plant would germinate and grow in salt environments. The overall germination of L. spicata showed that native microbes from high salinity sites positively affect the growth of plants in saltwater. Germination rate was significantly higher (25.8 %) in plants with microbes compared to control plants. Both saltwater exposure and microbial presence had a significant effect on plant growth, suggesting that the impact of saltwater on plant growth depends on the presence of microbes. Our results revealed a significant decrease in the number of microbial colony-forming units (CFUs) in response to saltwater treatment (p < 0.001). Both fungal and bacterial CFUs were significantly reduced in saltwater-treated soils compared to freshwater soils. These findings highlight the potential role of native soil microbes in enhancing plant resilience to salinity stress, offering valuable insights for improving plant survival and productivity in increasingly saline environments.},
}

@article {pmid40382874,
year = {2025},
author = {Miao, S and Zhang, Y and Wu, L and Wang, Y and Zuo, J},
title = {Resistance induction potency assessment of antibiotic production wastewater and associated resistome shaping mechanisms.},
journal = {Water research},
volume = {283},
number = {},
pages = {123811},
doi = {10.1016/j.watres.2025.123811},
pmid = {40382874},
issn = {1879-2448},
abstract = {Antibiotic production wastewater (APW) contains multiple substances known to select for and facilitate horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs); however, whether these substances can induce the evolution of antibiotic resistance in real wastewater environments and the fate of such resistance induction potency during the treatment process are poorly understood, nor are its relationship with wastewater quality parameters and function in shaping the antibiotic resistome. In this study, the impacts of filter-sterilized APW and municipal wastewater on the resistance selection of Escherichia coli and the transfer dynamics of conjugative RP4 plasmid-borne ARGs across indigenous sludge communities were evaluated. The resistance development and transfer processes were accelerated in APW owing to enhanced growth inhibition, oxidative stress, and membrane permeability, with antibiotic concentrations much lower than their minimum inhibition concentrations. The effects were reduced simultaneously with the removal of COD and NH3N, but APW effluents still exhibited significant resistance induction potency with wastewater quality parameters meeting discharge standards. In contrast, municipal wastewater did not result in any detectable changes. Based on the metagenomic assembly and binning, stronger resistance induction potency in the antibiotic production wastewater treatment plant endowed indigenous sludge and effluent with greater accumulation, genetic mobility, and pathogenic accessibility of ARGs than in the municipal wastewater treatment plant. Antibiotic resistome assembly was determined primarily by deterministic processes, driven jointly by resistance induction potency, mobilome variance, and microbiome shifts. These results provide novel insights into the application of bioassays to comprehensively evaluate the antibiotic resistance induction effects of APW and their relationships with the resistome to manage risks during the treatment process.},
}

@article {pmid40382784,
year = {2025},
author = {El-Bayoumy, K and Christensen, N and Broach, J and Meyers, C and Stairs, D and Machtay, M and Hu, J and Bitzer, ZT and Schell, TD and Chen, KM and Sun, YW and Desai, D and Walter, V and Zhu, J},
title = {Current Challenges and Potential Opportunities for Interception and Prevention of Head and Neck Cancer.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgaf025},
pmid = {40382784},
issn = {1460-2180},
abstract = {Globally, the incidence of head and neck squamous cell carcinoma (HNSCC) has increased over recent decades and is projected to continue to rise, largely driven by increases in oropharyngeal squamous cell carcinoma (OPSCC) which is linked to HPV infection. HPV infection is also involved in the development of other cancers (anogenital and cervical) and almost 100% of cervical cancer patients are positive for HPV. OPSCC is the most common HPV-associated cancer in men and has exceeded the incidence of cervical cancer cases in women in the US. Our knowledge of the carcinogenesis process from HPV infection to OPSCC development has been primarily extrapolated from cervical cancer models. While the cooperation of tobacco smoking and HPV infection is documented in cervical cancer, mechanistic studies to address this interaction in management and control of HNSCC are scarce and are also extrapolated from cervical cancer models. The molecular heterogeneity of HNSCC constitutes a tremendous challenge, and despite advances in several fronts in the management and control of HSNCC, short- and long-term treatment-associated morbidities remain substantial. In addition to deaths directly caused by this disease, survivors of this cancer have the second highest rate of suicide compared with other cancers survivors. Given the existing gaps in our knowledge and the current clinical challenges, future studies including a number of new conceptual and methodological elements discussed in this review can lead to the discovery of biomarkers for early detection of the disease and novel strategies which will advance our knowledge to intercept and prevent HNSCC.},
}

@article {pmid40382763,
year = {2025},
author = {Alizadeh, M and Wong, U and Siaton, BC and France, MT and Patil, SA and George, L and Hudhud, D and Motwani, K and Scott, WH and Raufman, JP and von Rosenvinge, EC and Cross, RK and Ravel, J},
title = {The intestinal mucosa-associated microbiota in IBD-associated arthritis displays lower relative abundance of Roseburia intestinalis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2505114},
doi = {10.1080/19490976.2025.2505114},
pmid = {40382763},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/complications ; *Intestinal Mucosa/microbiology ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; *Arthritis/microbiology ; Bacteria/classification/isolation & purification/genetics ; Feces/microbiology ; Aged ; *Clostridiales/isolation & purification/genetics/classification ; },
abstract = {The most common extra-intestinal manifestation (EIM) of inflammatory bowel disease (IBD), IBD-associated arthritis (IAA), occurs in 25-40% of patients and can be debilitating. In IBD, mucosal and stool microbiota richness is decreased, and compositional changes can precede or accompany disease onset. Likewise, spondyloarthritides are associated with altered gut microbiota, with overlapping bacterial signatures observed in IBD, suggesting key shared microbial factors are involved in both conditions. Much has been learned about the role of the intestinal microbiome in IBD, but less is known regarding its role in IAA. To address this knowledge gap, we analyzed the mucosa-associated intestinal microbiota of participants enrolled in the LOCATION-IBD cohort. Microbiota composition was established using 16S rRNA gene amplicon sequencing of intestinal biopsy samples taken from participants with IBD, with or without arthropathy. Microbiota samples clustered predominantly by participant, and similar taxa were present across the colon. The mucosal intestinal microbiota of females with IAA displayed a lower relative abundance of R. intestinalis, while males with IAA had a higher relative abundance of Corynebacterium, even when controlling for IBD-type, whether samples were taken from a site of inflammation and intestinal location. These findings indicate the mucosa-associated intestinal microbiota is associated with IAA in a sex-specific manner.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
*Inflammatory Bowel Diseases/microbiology/complications
*Intestinal Mucosa/microbiology
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
*Arthritis/microbiology
Bacteria/classification/isolation & purification/genetics
Feces/microbiology
Aged
*Clostridiales/isolation & purification/genetics/classification

@article {pmid40382722,
year = {2025},
author = {Cheng, HS and Tey, YH and Hu, SY and Yeo, AYN and Ngo, ZH and Kim, JHS and Tan, NS},
title = {Advancements and Challenges in Modeling Mechanobiology in Intestinal Host-Microbiota Interaction.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.4c20961},
pmid = {40382722},
issn = {1944-8252},
abstract = {The gastrointestinal tract is a dynamic biomechanical environment where physical forces, cellular processes, and microbial interactions converge to shape the gut health and disease. In this review, we examine the unique mechanical properties of the gut, including peristalsis, viscoelasticity, shear stress, and tissue stiffness, and their roles in modulating host mechanosignaling and microbial behavior under physiological and pathological conditions. We discuss how these mechanical forces regulate gut epithelial integrity, immune responses, and microbial colonization, leading to distinct ecological niches across different intestinal segments. Furthermore, we highlight recent advancements in 3D culture systems and gut-on-a-chip models that accurately recapitulate the complex interplay between biomechanics and gut microbiota. By elucidating the intricate relationship between mechanobiology and gut function, this review underscores the potential for mechanotherapeutic strategies to modulate host-microbe interactions, offering promising avenues for the prevention and treatment of disorders such as inflammatory bowel disease, irritable bowel syndrome, and colorectal cancer.},
}

@article {pmid40382665,
year = {2025},
author = {Xia, XX and Li, CX and Guo, HR},
title = {Association between oral microbiome diversity and chronic obstructive pulmonary disease in the US population.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {557},
pmid = {40382665},
issn = {1479-5876},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/epidemiology ; *Microbiota/genetics ; United States/epidemiology ; Female ; Male ; Middle Aged ; *Mouth/microbiology ; Phylogeny ; *Biodiversity ; Risk Factors ; Aged ; Cross-Sectional Studies ; Adult ; Nutrition Surveys ; },
abstract = {BACKGROUND: There is a dearth of population-based studies on the association between the diversity of the oral microbiome and the risk of chronic obstructive pulmonary disease (COPD). The study aims to investigate the association between oral microbiome diversity and COPD.

METHODS: In this cross-sectional study, data from the National Health and Nutrition Examination Survey (NHANES 2009-2012) were analyzed. The association between the oral microbiome α-diversity and COPD risk was examined via multivariable logistic regression, with Restricted cubic splines revealing potential non-linear trends. The β-diversity disparities between COPD and non-COPD groups were delineated using Principal Coordinate Analysis (PCoA) and Permutational Multivariate Analysis of Variance (PERMANOVA).

RESULTS: A total of 6061 participants were included in this study. For α-diversity, the observed ASVs were significantly associated with COPD risk (OR = 0.964, 95%CI: 0.936-0.993, P = 0.016). Similarly, Faith's phylogenetic Diversity showed a significant association with COPD risk (OR = 0.955, 95%CI: 0.919-0.993, P = 0.020). The Shannon-Weiner index was also associated with COPD risk (OR = 0.829, 95%CI: 0.702-0.981, P = 0.029). For β-diversity, PCoA and PERMANOVA analysis showed statistically significant differences in Bray-Curtis, unweighted, and weighted UniFrac distances (all P < 0.01) between the COPD and non-COPD groups.

CONCLUSIONS: Significant differences in oral microbiome α-diversity and β-diversity were found between COPD and non-COPD populations, with α-diversity (observed ASVs, Faith's Phylogenetic Diversity, Shannon-Weiner index) being negatively associated with the risk of COPD.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/epidemiology
*Microbiota/genetics
United States/epidemiology
Female
Male
Middle Aged
*Mouth/microbiology
Phylogeny
*Biodiversity
Risk Factors
Aged
Cross-Sectional Studies
Adult
Nutrition Surveys

@article {pmid40382661,
year = {2025},
author = {Trzebny, A and Taylor, AD and Herren, JK and Björkroth, JK and Jedut, S and Dabert, M},
title = {Microsporidian infection of mosquito larvae changes the host-associated microbiome towards the synthesis of antimicrobial factors.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {178},
pmid = {40382661},
issn = {1756-3305},
support = {2024/53/B/NZ6/01181//Narodowe Centrum Nauki/ ; 140/04/POB2/0002//Initiative of Excellence-Research University/ ; },
mesh = {Animals ; Larva/microbiology/parasitology ; *Microsporidia/physiology ; *Culex/microbiology/parasitology ; *Microbiota ; Mosquito Vectors/microbiology ; Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Antimicrobial Peptides/biosynthesis ; Host Microbial Interactions ; },
abstract = {BACKGROUND: Microsporidians (Microsporidia) are a group of obligate intracellular parasites that commonly infect mosquitoes. Recently, it has been shown that infection by these parasites can alter the composition and functionality of the mosquito-associated microbiome. The host-associated microbiome of the mosquito can play a pivotal role in various physiological processes of this host, including its vector competence for pathogens. Thus, understanding how microsporidians shape the mosquito microbiome may be crucial for elucidating interactions between these parasites and their mosquito hosts, which are also vectors for other parasites and pathogens.

METHODS: The effects of microsporidian infection on the microbiome structure and functionality of Culex pipiens and Culex torrentium larvae under semi-natural conditions were examined. The host-associated microbiome of Cx. pipiens (n = 498) and Cx. torrentium (n = 465) larvae, including that of the 97 infected individuals of these samples, was analysed using 16S DNA profiling and functional prediction analysis.

RESULTS: Microbiome network analysis revealed that, in the microsporidian-positive larvae, host microbial communities consistently grouped within a common bacterial module that included Aerococcaceae, Lactobacillaceae, Microbacteriaceae, Myxococcaceae, and Polyangiaceae. Indicator species analysis revealed two strong positive correlations between microsporidian infection and the presence of Weissella cf. viridescens and Wolbachia pipientis. Functional predictions of microbiome content showed enrichment in biosynthetic pathways for ansamycin and vancomycin antibiotic groups in infected larvae. Furthermore, the MexJK-OprM multidrug-resistance module was exclusively present in the infected larvae, while carbapenem- and vancomycin-resistance modules were specific to the microsporidian-free larvae.

CONCLUSIONS: Our results demonstrate that microsporidian infection alters the microbial community composition in mosquito larvae. Moreover, they show that microsporidian infection can increase the antimicrobial capabilities of the host-associated microbiome. These results provide novel insights into host microbiome-parasite interactions and have potential implications for the vector competencies of mosquitoes.},
}

Animals
Larva/microbiology/parasitology
*Microsporidia/physiology
*Culex/microbiology/parasitology
*Microbiota
Mosquito Vectors/microbiology
Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Antimicrobial Peptides/biosynthesis
Host Microbial Interactions

@article {pmid40382531,
year = {2025},
author = {Hasegawa, R and Poulin, R and Salloum, PM},
title = {Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {45},
pmid = {40382531},
issn = {1432-184X},
support = {202460294//Japan Society for the Promotion of Science/ ; UOO2113//Marsden Fund/ ; UOO2113//Marsden Fund/ ; },
mesh = {Animals ; *Trematoda/microbiology/classification ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Snails/parasitology/microbiology ; Phylogeny ; },
abstract = {Elucidating the specific processes and drivers of community assembly in the host microbiome is essential to fully understand host biology. Toward this goal, an important first step is to describe co-occurrence patterns among different microbial taxa, which can be driven by numerous factors, such as host identity. While host identity can be an important influential factor on co-occurrence patterns, a limited number of studies have explored the relative importance of host identity after controlling for other environmental factors. Here, we examined microbial co-occurrence patterns in four phylogenetically distinct trematode species living within the same snail species, collected concomitantly from the same habitat. Our previous study determined that all these trematodes shared some bacterial taxa, and the relative abundance of microbial taxa differed among trematodes, possibly due to differences in their eco-physiological traits. Here, we specifically predict that pairwise microbial co-occurrence patterns also vary among trematode host species. Our results showed that co-occurrence patterns among eight microbial families varied greatly among the four trematode hosts, with some microbial families co-occurring in some trematode species, whereas no such patterns were observed in other trematodes. Our study suggests that the habitat identity (trematode species) and its associated biotic characteristics, such as physiological and ecological traits, can determine co-occurrence patterns among microbial taxa, with substantial effects on local community composition.},
}

Animals
*Trematoda/microbiology/classification
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Snails/parasitology/microbiology
Phylogeny

@article {pmid40382475,
year = {2025},
author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG},
title = {The Microbial Ecology of Antarctic Sponges.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {44},
pmid = {40382475},
issn = {1432-184X},
mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; Ecosystem ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.},
}

*Porifera/microbiology
Animals
Antarctic Regions
*Microbiota
Symbiosis
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
Ecosystem
Fungi/classification/genetics/isolation & purification

@article {pmid40382082,
year = {2025},
author = {Zhang, X and Wang, Y and Zhang, M and Liu, B and Li, X and Zhao, J and Qiao, W and Liu, Y and Liu, Y and Chen, L},
title = {Association between fat-soluble vitamins in breast milk and neonatal gut microbiome in Tibetan mother-infant dyads during the first month postnatal.},
journal = {Food research international (Ottawa, Ont.)},
volume = {212},
number = {},
pages = {116350},
doi = {10.1016/j.foodres.2025.116350},
pmid = {40382082},
issn = {1873-7145},
mesh = {Humans ; *Milk, Human/chemistry ; *Gastrointestinal Microbiome/physiology ; Tibet ; Female ; Infant, Newborn ; Infant ; Adult ; *Vitamins/analysis ; Feces/microbiology ; Male ; Lactation ; Breast Feeding ; Vitamin A/analysis ; Colostrum/chemistry ; Vitamin E/analysis ; Infant Nutritional Physiological Phenomena ; Vitamin D/analysis ; Mothers ; },
abstract = {The Tibetan Plateau is a high-altitude environment characterized by hypoxic conditions, strong ultraviolet rays, and significant temperature variations that affect the well-being of local residents, including mother-infant dyads. Adaptive evolution through lifestyle and dietary patterns plays an important role in nutrition during the maternal lactation period, which offers unique merits for investigation at the intersection of environmental and nutritional fields. Specifically, changes in the nutrient composition of human milk among Tibetan lactating mothers and their associated consequences for infants provide insight into early nutrition research and infant food production. In this study, the concentrations of vitamins A, D, E, and β-carotene in the human milk of Tibetan mothers, as well as the fecal microbiome profiles of their infants, were analyzed within the first month postnatal. The results showed that the fat-soluble vitamins in Tibetan human milk were at satisfactory levels, particularly during the colostrum stage, which may be attributed to the advantages of their dietary pattern and dwelling environment. Dynamic changes in the gut microbiota composition of Tibetan infants were observed, with the phyla Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria being relatively abundant. The abundance of Bifidobacterium increased as infants aged within the first month postnatal. Correlations were found between the fat-soluble vitamin composition in human milk and the characteristics of the infant gut microbiota, including alpha (α)-diversity indices and microbial abundances. These findings will help enhance the understanding of early nutrition under harsh natural conditions and will guide relevant innovations and improvements in the maternal and infant food industry.},
}

Humans
*Milk, Human/chemistry
*Gastrointestinal Microbiome/physiology
Tibet
Female
Infant, Newborn
Infant
Adult
*Vitamins/analysis
Feces/microbiology
Male
Lactation
Breast Feeding
Vitamin A/analysis
Colostrum/chemistry
Vitamin E/analysis
Infant Nutritional Physiological Phenomena
Vitamin D/analysis
Mothers

@article {pmid40382032,
year = {2025},
author = {Xu, H and Tang, Q and Fan, K and Liu, M and Wang, L and Mo, K and Xu, Z and Zhang, W},
title = {Microbiome-metabolome correlations across vertical stratification in Jiupei of strong-flavored baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {212},
number = {},
pages = {116395},
doi = {10.1016/j.foodres.2025.116395},
pmid = {40382032},
issn = {1873-7145},
mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Volatile Organic Compounds/analysis ; Bacteria/classification/metabolism/genetics ; Metabolomics ; *Wine/microbiology/analysis ; },
abstract = {The differences in the microbiota and metabolites from the different vertical stratification in Jiupei are obvious but not entirely clear. This study used high-throughput sequencing and metabolomics techniques to explore the microbiome and metabolites of varying vertical stratification in Jiupei and their relationships. The results showed that most beneficial metabolites, including pentadecanoic acid, ricinoleic acid, and epigallocatechin, were significantly higher in the lower Jiupei layer. Some volatile compounds gradually showed upregulation with increased Jiupei depth, mainly esters, ketones, and terpenoids. The bacterial community diversity of Jiupei decreased significantly with the increase in depth, Acetilactobacillus jinshanensis dominated the Jiupei bacterial community, and its relative abundance increased significantly (P < 0.05) with the rise of Jiupei depth (P < 0.05). The fungi Aspergillus oryzae (P = 0.057) and Byssochlamys spectabilis increased significantly, Dipodascus australiensis (P < 0.05), Pichia kudriavzevii (P = 0.08), and Dipodascus geotrichum (P < 0.05) gradually decreased. The correlation relationship analysis revealed that the dominant microbes that caused the metabolites and volatile compounds differences were the bacterium Acetilactobacillus jinshanensis and the fungus Aspergillus oryzae as well as Byssochlamys spectabilis, which may be through biosynthesis of other secondary metabolites and lipid metabolism to impact the Jiupei metabolites. The study demonstrated the microbiome and metabolite differences in three layers of Jiupei and the effect of microbes on the characteristic metabolite formation of strong-flavor baijiu.},
}

*Fermentation
*Microbiota
*Metabolome
Volatile Organic Compounds/analysis
Bacteria/classification/metabolism/genetics
Metabolomics
*Wine/microbiology/analysis

@article {pmid40381961,
year = {2025},
author = {Zhao, X and Lei, C and Wang, Y and Zhang, L and Tang, W and Li, Z and Jiang, L and Li, X},
title = {Impact of TLR5 Overexpression on Gut Microbiota and Metabolites: Insights into Salmonella Infection Outcomes.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107708},
doi = {10.1016/j.micpath.2025.107708},
pmid = {40381961},
issn = {1096-1208},
abstract = {BACKGROUND: The gut microbiome and the host immune system work together to maintain intestinal health and protect against infections. Toll-like receptor 5 (TLR5) recognizes bacterial flagellin and plays a crucial role in this network. However, the precise role of TLR5 in regulating gut microbiota and resistance to infection remains unclear. This study utilized a TLR5 intestine-specific overexpression mouse model to explore these interactions and their impact on Salmonella infection.

METHODS: TLR5 intestine-specific overexpression mice (TLR5+/+) and wild-type (WT) mice were infected with Salmonella to assess TLR5's protective role. Survival time, fecal Salmonella load, and intestinal tissue integrity were evaluated. Subsequently, 16S rRNA sequencing and LC-MS-based metabolomics were performed to analyze gut microbiota composition and fecal metabolites. Fecal microbiota transplantation (FMT) and metabolite transplantation experiments were conducted to evaluate the functional impact of microbiota and metabolites on resistance to infection.

RESULTS: TLR5 overexpression significantly improved survival time and reduced fecal Salmonella load, demonstrating its protective role against infection. 16S rRNA sequencing revealed enrichment of beneficial taxa, while metabolomic analysis identified altered metabolites in TLR5+/+ mice. Although fecal microbiota and metabolite transplantation did not fully replicate the protective effects, these experiments highlighted the important roles of microbiota and metabolites in infection outcomes, with limitations in transplantation likely affecting the results. These findings underscore the significance of microbiota and metabolites in TLR5-mediated gut immunity.

CONCLUSION: TLR5 overexpression significantly alters gut microbiota and metabolite profiles, contributing to improved infection outcomes. These findings highlight the critical roles of microbiota and metabolites in TLR5-mediated immunity and provide a foundation for exploring targeted strategies to enhance resistance against enteric pathogens.},
}

@article {pmid40381958,
year = {2025},
author = {Bolte, LA and Björk, JR and Gacesa, R and Weersma, RK},
title = {Pharmacomicrobiomics: The role of the gut microbiome in immunomodulation and cancer therapy.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.04.025},
pmid = {40381958},
issn = {1528-0012},
abstract = {There is a large heterogeneity among individuals in their therapeutic responses to the same drug and in the occurrence of adverse events. A key factor increasingly recognized to contribute to this variability is the gut microbiome. The gut microbiome can be regarded as a second genome, holding significant metabolic capacity. Consequently, the field of pharmacomicrobiomics has emerged as a natural extension of pharmacogenomics for studying variations in drug responses. Pharmacomicrobiomics explores the interaction of microbiome variation with drug response and disposition. The interaction between microbes and drugs is, however, complex and bidirectional. While drugs can directly alter microbial growth or influence gut microbiome composition and functionality, the gut microbiome also modulates drug responses directly through enzymatic activities and indirectly via host-mediated immune and metabolic mechanisms. Here we review recent studies that demonstrate the interaction between drugs and the gut microbiome, focusing on cancer immunotherapy and immunomodulation in the context of inflammatory bowel disease and solid organ transplantation. Since the gut microbiome is modifiable, pharmacomicrobiomics presents promising opportunities for optimizing therapeutic outcomes, with recent clinical trials highlighting fecal microbiota transplantation as a strategy to enhance the efficacy of immune checkpoint blockade. We also shed light on the future perspectives for patients arising from this field. While multiple lines of evidence already demonstrate that the gut microbiome interacts with drugs, and vice versa, thereby affecting treatment efficacy and safety, well-designed clinical studies and integrated in vivo and ex vivo models are necessary to obtain consistent results, improve clinical translation and further unlock the gut microbiome's potential to improve drug responses.},
}

@article {pmid40381872,
year = {2025},
author = {Barlowe, TS and Desai, S and Sanderford, AE and Holowka, T and Peery, AF and McGill, SK},
title = {Fulminant Clostridioides difficile Infection Following Fecal Microbiota Spores compared to Fecal Microbiota Transplant.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2025.03.027},
pmid = {40381872},
issn = {1542-7714},
}

@article {pmid40381742,
year = {2025},
author = {Lin, L and Huang, D and Huang, H and Xie, L and Huang, Y and Ye, C and Chu, L and Qiao, Y and Meng, X and Cai, S and Dong, H},
title = {Lung microbiota metabolite L-malic acid attenuates the airway inflammation in asthma by inhibiting ferroptosis.},
journal = {Toxicology and applied pharmacology},
volume = {},
number = {},
pages = {117396},
doi = {10.1016/j.taap.2025.117396},
pmid = {40381742},
issn = {1096-0333},
abstract = {Inhaled environmental allergens, such as house dust mites (HDM), have been shown to induce an inflammatory reaction, tissue injury, and increased airway sensitivity in the lungs, ultimately leading to the development of allergic asthma. The imbalance of respiratory microbiota and metabolites plays a crucial role in the progression of allergic asthma. However, there is limited knowledge available regarding the alterations in respiratory microbiota and metabolites and their impact on the host in the context of asthma. The aim of this study was to investigate the potential pathways involved in the development of asthma through the analysis of lung flora and metabolites. A mouse model of house dust mite (HDM)-induced asthma was established, and alveolar lavage samples were collected for microbiome 16S rRNA sequencing and untargeted metabolic analysis. Microbiological analyses indicated a significant alteration in the microbiota after 4 and 6 weeks of HDM nebulisation stimulation. This was characterized by a decrease in microbial diversity, as well as reductions in the relative proportion of Gallionella and Lactobacillus. Conversely, the abundance of Flavobacterium and Ralstonia increased in the HDM4W and HDM6W groups, respectively. Metabolomic analyses revealed seven distinct metabolites, among them L-malic acid, which were linked to signaling pathways in a mouse model of HDM-induced asthma. The correlation analysis demonstrated a positive association between L-malic acid and Rhodanobacter and Nocardioides. L-malic acid was discovered to be efficacious in reducing airway inflammation in mice with house dust mite-induced asthma. Further analysis revealed that this change was linked to lipid peroxidation and changes in ferroptosis markers, namely GPX4 and FTH. These findings suggest that L-malate inhibits ferroptosis. However, the introduction of ferroptosis inducers, such as Erastin, was observed to negate the beneficial effect of butyrate. In summary, this research implies that the respiratory microbiota metabolite L-malic acid lessens airway inflammation in asthma by inhibiting ferroptosis, offering a potential approach for managing asthma.},
}

@article {pmid40381618,
year = {2025},
author = {Kim, M and Kim, J and Lee, GS and Olinares, PDB and Airan, Y and Chow, JL and Park, J and Jeong, Y and Park, J and Chait, BT and Herzon, SB and Kim, CS and Kang, JY},
title = {Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin.},
journal = {Structure (London, England : 1993)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.str.2025.04.017},
pmid = {40381618},
issn = {1878-4186},
abstract = {Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway, known as pks or clb, the structural details of its biosynthetic enzymes remain limited, hindering our understanding of its biosynthesis and clinical application. In this study, we report the cryo-EM structures of two colibactin-producing PKS enzymes, ClbC and ClbI, captured in different reaction states using a substrate-mimic crosslinker. Our structural analysis revealed the binding sites of carrier protein (CP) domains of the ClbC and ClbI on their ketosynthase (KS) domains. Further, we identified a novel NRPS-PKS docking interaction between ClbI and its upstream enzyme, ClbH, mediated by the C-terminal peptide ClbH and the dimeric interface of ClbI, establishing a 1:2 stoichiometry. These findings advance our understanding of colibactin assembly line and provide broader insights into NRPS-PKS natural product biosynthesis mechanisms.},
}

@article {pmid40381485,
year = {2025},
author = {Hartjes, ED and Lim, YJ and Velenosi, TJ and Al, KF and Macklaim, JM and Kucey, AS and Reid, G and Burton, JP and Gloor, GB and Urquhart, BL},
title = {The impact of progressive chronic kidney disease on hepatic drug metabolism.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {53},
number = {6},
pages = {100085},
doi = {10.1016/j.dmd.2025.100085},
pmid = {40381485},
issn = {1521-009X},
abstract = {Nonrenal clearance pathways such as drug metabolism are decreased in severe chronic kidney disease (CKD). The impact of progression of CKD on hepatic drug metabolism is unknown. We characterized the effect of progressive CKD on hepatic cytochrome P450 expression and evaluated dysbiosis and uremia as kidney function declined. Rats fed control or CKD-inducing adenine diet were studied at 5 time points over 42 days. Cytochrome P450 expression and activity were compared with alterations in the (1) plasma and liver metabolome and (2) gut bacterial microbiota. CYP3A2 and CYP2C11 were downregulated in CKD by ≥76% (P < .001) concurrently with or slightly prior to CKD onset as defined by serum creatinine. Metabolite profiles were altered prior to changes in the gut microbiota, and gut-derived uremic toxins including indoxyl sulfate, phenyl sulfate, and 4-ethylphenyl sulfate correlated with CYP3A2 or CYP2C11 expression. Bacterial genera Turicibacter and Parabacteroides were identified as being characteristic of CKD. In conclusion, CYP3A2 and CYP2C11 are downregulated before dysbiosis and uremia. SIGNIFICANCE STATEMENT: This study describes the effect of progressive kidney disease on hepatic CYP2C11 and CYP3A2 enzyme expression and activity in a rat model of CKD. Expression and activity of drug metabolizing enzymes occurs prior to uremia or dysbiosis.},
}

@article {pmid40380289,
year = {2025},
author = {Amutuhaire, H and Faigenboim-Doron, A and Kraut-Cohen, J and Friedman, J and Cytryn, E},
title = {Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {52},
pmid = {40380289},
issn = {2524-6372},
abstract = {BACKGROUND: Soilborne fungal phytopathogens pose a significant threat to global food security. While chemical control remains an effective method for managing these pathogens, increasing regulations due to health and environmental concerns, along with rising fungicide resistance, have restricted their use, underscoring the urgent need for sustainable alternatives. The use of compost to enhance soil fertility and suppress plant diseases is well documented. Several studies have underlined the role of microorganisms in disease suppression, but the mechanisms facilitating this disease suppression remain unclear. We evaluated the impact of compost amendment on the composition and functional capacity of the rhizosphere microbiome in cucumber plants (Cucumis sativus) inoculated with Fusarium oxysporum f. sp. radicis-cucumerinum (FORC) under controlled greenhouse conditions using amplicon sequencing, shotgun metagenomic and culture-based techniques.

RESULTS: Compost amendment significantly reduced FORC-induced disease in cucumber relative to non-amended treatments. While FORC inoculation resulted in significant shifts in microbial (bacterial and fungal) community composition in the rhizosphere of non-amended plants, this phenomenon was substantially less pronounced in the rhizosphere of compost-amended plants. Specifically, compost amendment sustained the presence of Actinomycetota (Streptomyces, Actinomadura, Saccharomonospora, Pseudonocardia, Glycomyces, Thermobifida) and Bacillota (Planifilum, Novibacillus) in FORC inoculated plants, that diminished significantly in inoculated plants without compost. These taxa contained a myriad of non-ribosomal peptides and polyketides synthetases biosynthetic gene clusters (BGCs) with putative antimicrobial and iron-chelating functions. We successfully isolated two Streptomyces strains from FORC-suppressing compost amended rhizospheres that were almost identical to the Streptomyces bin2 (99% ortho ANI) metagenome assembled genome identified in the shotgun metagenome analysis. These strains produced extracellular metabolites that inhibited growth of FORC in-vitro and contained BGCs that encode for compounds with potential antimicrobial capacity.

CONCLUSIONS: Based on results presented in this study, we demonstrate that compost alleviates FORC-induced dysbiosis of the rhizosphere microbiome, maintaining abundance of specific bacterial taxa. These bacterial groups may contribute to disease suppression through a myriad of mechanisms including iron chelation and production of fungal antagonizing secondary metabolites.},
}

@article {pmid40380272,
year = {2025},
author = {Zhang, S and Zheng, N and Zhao, S and Wang, J},
title = {Allicin enhances urea-N conversion to microbial-N by inhibiting urease activity and modulating the rumen microbiome in cattle.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {124},
pmid = {40380272},
issn = {2049-2618},
support = {2023M743835//Project Funded by China Postdoctoral Science Foundation/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 2022YFD1301000//National Key Research and Development Program of China/ ; 2004DA125184G2406//State Key Laboratory of Animal Nutrition and Feeding/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/chemistry ; *Urease/antagonists & inhibitors/metabolism/chemistry ; *Rumen/microbiology ; *Urea/metabolism ; Disulfides/pharmacology ; *Nitrogen/metabolism ; Cattle ; Molecular Docking Simulation ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/metabolism/drug effects/classification/genetics ; Enzyme Inhibitors/pharmacology ; },
abstract = {BACKGROUND: Urea serves as a vital nonprotein nitrogen source in ruminant nutrition, but its efficient utilization is often hampered due to rapid urease activity in the rumen. This study explores the potential of allicin, a garlic-derived compound, as a urease inhibitor to improve urea nitrogen utilization. Enzyme inhibition kinetics and molecular docking were used to identify allicin's interaction sites on urease. Additionally, metagenomic and [15]N-urea metabolic flux analyses were conducted to evaluate allicin's impact on microbial populations and urea-N metabolism.

RESULTS: Allicin was identified as an inhibitor of ruminal urease, with an IC50 of 126.77 ± 1.21 μM. Molecular docking studies have shown that allicin forms hydrogen bonds with key urease residues, leading to the preemption of the urease active site and thus impeding urea binding. In a simulated rumen environment, allicin significantly reduced urea hydrolysis and ammonia production. Furthermore, allicin modified the rumen microbial community by inhibiting Prevotella species while promoting the growth of Ruminobacter species and Denitrobacterium detoxificans. A [15]N-urea metabolic flux analysis revealed that allicin facilitated the incorporation of urea-derived nitrogen into microbial amino acids and nucleotides.

CONCLUSION: Allicin effectively inhibits urease activity in the rumen, enhancing the conversion of urea-N into microbial biomass. These findings suggest that allicin has significant potential to optimize urea metabolism in the rumen, offering a novel strategy for improving ruminant nitrogen nutrition. Video Abstract.},
}

Animals
*Sulfinic Acids/pharmacology/chemistry
*Urease/antagonists & inhibitors/metabolism/chemistry
*Rumen/microbiology
*Urea/metabolism
Disulfides/pharmacology
*Nitrogen/metabolism
Cattle
Molecular Docking Simulation
*Gastrointestinal Microbiome/drug effects
*Bacteria/metabolism/drug effects/classification/genetics
Enzyme Inhibitors/pharmacology

@article {pmid40380167,
year = {2025},
author = {Philip, D and Hodgkiss, R and Radhakrishnan, SK and Sinha, A and Acharjee, A},
title = {Deciphering microbial and metabolic influences in gastrointestinal diseases-unveiling their roles in gastric cancer, colorectal cancer, and inflammatory bowel disease.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {549},
pmid = {40380167},
issn = {1479-5876},
mesh = {Humans ; *Stomach Neoplasms/microbiology/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Colorectal Neoplasms/microbiology/metabolism ; Gastrointestinal Microbiome ; Metabolome ; Machine Learning ; *Gastrointestinal Diseases/microbiology/metabolism ; Biomarkers/metabolism ; },
abstract = {INTRODUCTION: Gastrointestinal disorders (GIDs) affect nearly 40% of the global population, with gut microbiome-metabolome interactions playing a crucial role in gastric cancer (GC), colorectal cancer (CRC), and inflammatory bowel disease (IBD). This study aims to investigate how microbial and metabolic alterations contribute to disease development and assess whether biomarkers identified in one disease could potentially be used to predict another, highlighting cross-disease applicability.

METHODS: Microbiome and metabolome datasets from Erawijantari et al. (GC: n = 42, Healthy: n = 54), Franzosa et al. (IBD: n = 164, Healthy: n = 56), and Yachida et al. (CRC: n = 150, Healthy: n = 127) were subjected to three machine learning algorithms, eXtreme gradient boosting (XGBoost), Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO). Feature selection identified microbial and metabolite biomarkers unique to each disease and shared across conditions. A microbial community (MICOM) model simulated gut microbial growth and metabolite fluxes, revealing metabolic differences between healthy and diseased states. Finally, network analysis uncovered metabolite clusters associated with disease traits.

RESULTS: Combined machine learning models demonstrated strong predictive performance, with Random Forest achieving the highest Area Under the Curve(AUC) scores for GC(0.94[0.83-1.00]), CRC (0.75[0.62-0.86]), and IBD (0.93[0.86-0.98]). These models were then employed for cross-disease analysis, revealing that models trained on GC data successfully predicted IBD biomarkers, while CRC models predicted GC biomarkers with optimal performance scores.

CONCLUSION: These findings emphasize the potential of microbial and metabolic profiling in cross-disease characterization particularly for GIDs, advancing biomarker discovery for improved diagnostics and targeted therapies.},
}

Humans
*Stomach Neoplasms/microbiology/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism
*Colorectal Neoplasms/microbiology/metabolism
Gastrointestinal Microbiome
Metabolome
Machine Learning
*Gastrointestinal Diseases/microbiology/metabolism
Biomarkers/metabolism

@article {pmid40379933,
year = {2025},
author = {Wroot, E and Chapman, JA and Young, GR and Berrington, JE and Stewart, CJ},
title = {Opportunities for microbiome-based therapeutics in preterm infants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40379933},
issn = {2058-5276},
support = {221745/Z/20/Z//Wellcome Trust (Wellcome)/ ; NA//Lister Institute of Preventive Medicine/ ; },
}

@article {pmid40379875,
year = {2025},
author = {Guédon, G and Charron-Bourgoin, F and Lacroix, T and Hamadouche, T and Soler, N and Douzi, B and Chiapello, H and Leblond-Bourget, N},
title = {Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17013},
pmid = {40379875},
issn = {2045-2322},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Genome, Bacterial ; *Faecalibacterium/genetics/physiology ; *Conjugation, Genetic ; *Adaptation, Physiological/genetics ; Feces/microbiology ; Phylogeny ; },
abstract = {Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14-23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe[3+], carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.},
}

*Gastrointestinal Microbiome/genetics
Humans
Genome, Bacterial
*Faecalibacterium/genetics/physiology
*Conjugation, Genetic
*Adaptation, Physiological/genetics
Feces/microbiology
Phylogeny

@article {pmid40379732,
year = {2025},
author = {Dyroff, AI and López-Valiñas, Á and Magalhaes, HB and Podico, G and Canisso, IF and Almiñana, C and Bauersachs, S},
title = {Comparison of RNA- and DNA-based 16S amplicon sequencing to find the optimal approach for the analysis of the uterine microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {17037},
pmid = {40379732},
issn = {2045-2322},
support = {200534//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {Female ; Animals ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Uterus/microbiology ; *DNA, Bacterial/genetics ; Horses ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; RNA, Bacterial/genetics ; },
abstract = {Studies in humans and large animals indicate a relationship between the uterine microbiome composition and endometrial receptivity. Despite many studies have been performed, the analysis of the uterine microbiome remains challenging due to the very low microbial biomass. Studies in other biological systems showed that RNA-based microbiome analysis complements DNA-based results and provides information about active bacteria in a sample. Thus, the aim of this study was to establish a highly sensitive and specific 16S rRNA gene V3-V4 amplicon PCR from equine uterine cytobrush samples and to compare DNA- and RNA-based 16S rRNA microbiome analysis. An optimized 16S rRNA gene V3-V4 amplicon PCR protocol from equine uterine cytobrush samples was developed, which was able to detect less than 38 bacterial genome copies using a bacterial DNA community standard. For the RNA-based amplicon generation protocol starting from cDNA, at least a 10-fold higher sensitivity was estimated compared to DNA-based approach. The comparison of using RNA and DNA isolated from the same uterine cytobrush samples as input for 16S V3-V4 amplicon sequencing revealed a much higher number of amplicon sequence variants as well as taxonomic units for the RNA-based approach. This resulted in significant differences in alpha (Simpson, Chao1) and beta diversity between RNA- and DNA-based analysis. Differential abundance analysis revealed significant differences between DNA and RNA samples at all taxonomic levels. Despite these differences, the overall microbiome composition was similar between the paired DNA and RNA samples. Many differences were probably found due to the higher sensitivity of the RNA-based approach. Furthermore, the DNA-based analysis is biased by the rRNA gene copy numbers (1-21), and the RNA-based analysis by the number of ribosomes per cell, which was reflected in the differences in the microbiome composition between the approaches. In addition, the results suggested that the DNA-based analysis is detecting cell-free bacterial DNA and/or DNA of dead bacteria that could be present in the samples. Altogether, the obtained results indicate advantages of a combined DNA- and RNA-based microbiome analysis, offering complementary and valuable information in the context of fertility-related studies of the uterine microbiome.},
}

Female
Animals
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Uterus/microbiology
*DNA, Bacterial/genetics
Horses
*Bacteria/genetics/classification
Sequence Analysis, DNA/methods
RNA, Bacterial/genetics

@article {pmid40379554,
year = {2025},
author = {Zhao, T and Jia, X and Nepal, J and Attard, E and Guyoneaud, R and Elzenga, JTM and Falcão Salles, J},
title = {A microbiome perspective of Grime's triangle and plant ecological trade-offs.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.009},
pmid = {40379554},
issn = {1878-4372},
abstract = {Mutualistic interactions between plants and microbiomes are vital for plant growth and resilience. However, traditional breeding has undermined these interactions. Here, we explore the Grime's triangle from a microbiome perspective and discuss how traits from stress-tolerant species can aid in identifying cultivars with enhanced microbiome interactions.},
}

@article {pmid40379204,
year = {2025},
author = {Argenta, N and Clark, KF},
title = {Shell bacterial community dynamics suggest that American lobster (Homarus americanus) impoundment shell disease is caused by a dysbiosis.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108355},
doi = {10.1016/j.jip.2025.108355},
pmid = {40379204},
issn = {1096-0805},
abstract = {Impoundment shell disease (ISD) in the American lobster (Homarus americanus) is a distinct pathological condition from the more well-known epizootic shell disease. It is commonly observed at low prevalences in live American lobsters held overwinter in tidal pounds and significantly reduces their economic value. Impoundment shell disease was originally described in 1937; however, its etiology remains unclear. The main goal of this study was to characterize the bacterial community associated with ISD in Canadian lobsters. Lobsters were collected from a pound in southwest Nova Scotia, Canada, and the full 16S rRNA gene of bacterial communities from lesion and healthy shell areas of asymptomatic (As), moderately symptomatic (MS) and severely symptomatic (SS) animals was sequenced. Pielou evenness and Shannon diversity indexes of alpha-diversity were higher in healthy areas compared to lesion areas. Beta-diversity metrics indicate that the bacterial diversity differences are driven mainly by the relative abundance of a small number of bacteria, rather than the specific taxa present in the samples. Taxa were designated as being potentially involved with ISD based on their relative frequency, relative abundance or being core bacteriome in the lesion shell area. Among those found in this study, Tenacibaculum and Vibrio were previously described in ISD lesions; but others, such as Cellvibrionaceae, Polaribacter, Maribacter and Sulfitobacter were not. Altogether, the findings of this study indicate that ISD is driven by dysbiosis. Moreover, the inconsistency of taxa with previous studies may indicate that ISD consists of a combination of specific functional groups of bacteria, rather specific taxa.},
}

@article {pmid40378940,
year = {2025},
author = {Zhao, Q and Duan, Z and Lai, R and Ma, P},
title = {Novel microbially transformed bile acids: biosynthesis, structure, and function.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107775},
doi = {10.1016/j.phrs.2025.107775},
pmid = {40378940},
issn = {1096-1186},
abstract = {The roles of gut microbiota and microbially modified bile acids in human health have become widely recognized. In the last five years, various microbially modified bile acids (e.g., proteinogenic amino-conjugated bile acids, polyamine-conjugated bile acids, neuroactive amine-conjugated bile acids, methylcysteamine-conjugated bile acid, acylated bile acids, dicarboxylic acid-conjugated bile acids, lithocholic acid (LCA) derivatives) were identified and evaluated, which greatly enriched the mammalian bile acid pool and the bioactivity of bile acids. The structure, enzyme, function, clinical reports of these bile acids, and the bacteria to produce these bile acids were summarized in this review. These novel bile acids had various functions including immunoregulation, receptor regulator, antimicrobial activity, and microbial communities regulating effect. 70, 4, 1, 11, 19, 41, 43, 9, 10 species were observed to produce proteinogenic amino-conjugated bile acids, neuroactive amine-conjugated bile acids, methylcysteamine-conjugated bile acid, acylated bile acids, dicarboxylic acid-conjugated bile acids, 3-oxoLCA, isoLCA, 3-oxoalloLCA, and isoalloLCA, respectively. The current review has shed new light on discovering new bile acid derivatives as drug candidates. These microbially modified bile acids may play important roles in disease such as sleeve gastrectomy, fatty acid, inflammatory bowel disease, cystic fibrosis, and type 2 diabetes, which may also participate in normal physiological processes such as growth of infants, longevity, and dietary habits.},
}

@article {pmid40378938,
year = {2025},
author = {Feng, Y and Kim, JW and Xie, W},
title = {The intestinal functions of PXR and CAR.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107779},
doi = {10.1016/j.phrs.2025.107779},
pmid = {40378938},
issn = {1096-1186},
abstract = {Pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are so-called xenobiotic nuclear receptors that play pivotal roles in xenobiotic metabolism and detoxification. Both receptors, highly expressed in the liver and intestine, also have endobiotic functions by regulating the homeostasis of endogenous chemicals. While their hepatic functions are well-documented, the functional roles of PXR and CAR in the gastrointestinal tract are less understood. This review highlights the intestinal functions of PXR and CAR, focusing on their involvement in colon cancer, host-microbiome interactions, inflammation, and gut barrier integrity. PXR exhibits dual roles in colon cancer, acting either as a tumor suppressor by inducing cell-cycle arrest or as a promoter of cancer aggressiveness through activating the FGF19 signaling. CAR, on the other hand, regulates intestinal barrier integrity and immune responses, particularly in the context of inflammatory bowel disease (IBD). Both PXR and CAR interact with gut microbiota, modulating microbial composition and the production of metabolites, such as indole-3-propionic acid (IPA) that influences the gut barrier function and inflammation. Activation of PXR also mitigates intestinal inflammation by antagonizing the NF-κB signaling, while CAR activation affects bile acid metabolism and T-cell homeostasis. These findings underscore the complex and context-dependent roles of PXR and CAR in the intestinal tracts, offering potential therapeutic targets for gastrointestinal diseases.},
}

@article {pmid40378921,
year = {2025},
author = {Wong, SY and Estevinho, MM and Heaney, T and Marshall, AA and Giselbrecht, E and Daniel, SG and Zhou, C and Rosas-Villegas, A and Jang, KK and Yang, H and Mabel Ko, H and Paulson, JD and Ding, Y and Bittinger, K and Cho, JH and Lewis, JD and Ramanan, D and Cadwell, K},
title = {Goblet cell loss linked to NOD2 and secondary resection in Crohn's disease is induced by dysbiosis and epithelial MyD88.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101533},
doi = {10.1016/j.jcmgh.2025.101533},
pmid = {40378921},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: The role of goblet cells in small intestinal inflammation in Crohn's disease is unknown. Polymorphisms of NOD2 confer risk for Crohn's disease (CD) and associate with small intestinal disease location. We previously showed in mice that Nod2 deficiency leads to overexpansion of Phocaeicola vulgatus in the gut and downstream goblet cell defects, which preceded small intestinal inflammation. In this study, we ask whether goblet cell defects occur in CD patients with NOD2 polymorphisms and investigate in mice how P. vulgatus signals through the intestinal epithelium.

METHODS: We performed a retrospective study of patients with CD to assess clinical outcomes and goblet cell histology by NOD2 status. We evaluated the contribution of microbiota and MyD88 signaling in the intestinal epithelium to goblet cell defects in the setting of Nod2 deficiency using genetic mouse models and germ-free mice.

RESULTS: In patients with CD who have undergone ileocolic resection, NOD2 risk alleles confer a risk for re-operation (OR 8.12, P = .047) and for increased pERK and goblet cell defects in uninflamed ileal tissue. We show that patients with CD with ileal involvement harbor P. vulgatus regardless of NOD2 risk allele status. We show that intestinal epithelial MyD88 and TLR4 are required for goblet cell defects in Nod2[-/-] mice harboring P. vulgatus. Finally, we show that P. vulgatus requires complex microbiota to exert its effects in Nod2-deficient mice.

CONCLUSIONS: Goblet cell defects may be a harbinger of small intestinal inflammation in CD patients, particularly in the postoperative setting. Our findings in mice show that small intestinal goblet cell loss associated with Nod2 mutation is induced by microbiome dysbiosis and epithelial MyD88, in part due to TLR4 signaling.},
}

@article {pmid40378786,
year = {2025},
author = {Chmolowska, D and Wasak-Sęk, K and Chroňáková, A and Bahram, M and Choczyński, M and Tedersoo, L},
title = {Soil and its microbiome in translocated meadows in the context of habitats in the receptor area.},
journal = {Journal of environmental management},
volume = {386},
number = {},
pages = {125714},
doi = {10.1016/j.jenvman.2025.125714},
pmid = {40378786},
issn = {1095-8630},
abstract = {Turf translocation, which is undertaken to mitigate the destruction of valuable habitats, can challenge the soil biota. We investigated translocated protected Molinion meadows in the context of the surrounding environments. Soil and soil microorganisms were examined in meadows translocated four years earlier to a habitat garden in recycled land. Neighbouring habitats, comprised of woodland, cropland and fallow, represented the receptor area, while meadows that remained near the donor area were treated as reference areas. The soil moisture, compaction, reactivity and nutrient availability were examined. The microbial properties studied included taxon-specific markers for a quantitative PCR and Fatty Acid Analysis, N transformation (nitrification potential and ammonia oxygenase gene quantification), as well as the composition and diversity of bacteria, archaea, fungi and protists through soil DNA metabarcoding. The translocated soils were more compacted and had smaller water retention, which impacted the soil communities. A switch from N immobilisation to ammonification and a high diversity of fungi, including a greater richness of saprotrophic and symbiotrophic species occurred, with a higher relative abundance of Ascomycota. Amendments in Stramenopila, Chlorophyta and Alveolata communities were present. A low ratio of ammonia oxidising archaea and bacteria (AOA:AOB; 0.4 translocated vs. 4.9 reference) indicated a degradation of the wet meadow status, which created a suitable environment for copiotrophs. The initial increase in biodiversity pointed out habitat deterioration leading to the loss of specific, protected communities. The use of 'omics' was a sensitive indicator of changes that occurred at the level of the microbiome structure rather than the biomass.},
}

@article {pmid40378579,
year = {2025},
author = {Davison, A and Reimann, F and Gribble, FM},
title = {Molecular mechanisms of stimulus detection and secretion in enteroendocrine cells.},
journal = {Current opinion in neurobiology},
volume = {92},
number = {},
pages = {103045},
doi = {10.1016/j.conb.2025.103045},
pmid = {40378579},
issn = {1873-6882},
abstract = {Enteroendocrine cells (EECs) secrete over 20 different gut hormones in response to changes to the gut environment. They detect a range of nutritional stimuli through activation of a host of nutrient-sensing G-protein-coupled receptors and electrogenic nutrient cotransport. These activate intracellular signalling pathways which converge on membrane depolarisation and action potential generation, which elicit secretion. Emerging evidence has demonstrated that EECs also respond to non-nutritional stimuli, including mechanosensation, pH changes, and metabolites produced by the gut microbiome. EECs are polyhormonal cells, in which hormone expression is plastic and dependent on location in the gut. Hormones and small-molecule neurotransmitters secreted by EECs can activate extrinsic vagal afferents, modulating central processes such as appetite and food preference. While neuronal afferents are sometimes found in close proximity to EECs, the extent to which EEC/neuronal connections recapitulate traditional synaptic connections remains undefined.},
}

@article {pmid40378468,
year = {2025},
author = {Siddiquee, M and Cornelius, S and Seo, Y and Bullerjahn, GS and Bridgeman, TB and Sudman, M and Kang, DW},
title = {Uncovering microbial interactions in a persistent Planktothrix bloom: Towards early biomarker identification in hypereutrophic lakes.},
journal = {Water research},
volume = {283},
number = {},
pages = {123683},
doi = {10.1016/j.watres.2025.123683},
pmid = {40378468},
issn = {1879-2448},
abstract = {Cyanobacterial harmful algal blooms pose significant threats to global water supplies, ecosystems, and economies. Among the harmful cyanobacteria, Planktothrix, a resilient and toxin-producing filamentous cyanobacterium, has garnered increasing attention. However, an understanding of the entire microbiome, particularly the phycosphere surrounding Planktothrix blooms, remains largely unexplored. To the best of our knowledge, this is the first comprehensive study combining 16S rDNA and fungal internal transcribed spacer amplicon sequencing and shotgun metagenomics to elucidate Planktothrix bloom microbiomes and identify potential microbial or functional biomarkers for CyanoHABs. Our observations revealed that a summer bloom in Grand Lake St. Marys was initiated with Dolichospermum and then shifted to Planktothrix dominance. This transition was associated with nitrogen metabolism genes, suggesting that nitrogen plays a key role in bloom persistence through interactions among nitrogen-fixing bacteria, ammonia-oxidizing archaea, anammox bacteria, and denitrifiers. Additionally, metagenomic data revealed a strong positive correlation of toxin concentration with carbohydrate-nitrogen-sulfur-fatty acid associated metabolic pathways and a strong negative correlation with pollutant degradation pathways. Intriguingly, diazotrophic methane-related microbes were detected, which opens discussion on potential symbiosis that couples nitrogen and carbon metabolism. Toxin-degrading bacteria, such as Polynucleobacter and Acidovorax, were positively correlated with fungi like Vishniacozyma, proposing their cooperative roles during bloom events. Notably, Rhodobacter, a photosynthetic purple non-sulfur bacterium, showed strong negative correlations with both Planktothrix and the toxin-producing gene mcyE, positioning it as a promising biomarker for early bloom detection. Overall, this study advances the understanding of Planktothrix-dominated bloom ecology and highlights microbial signatures for proactive CyanoHAB management in freshwater systems.},
}

@article {pmid40378358,
year = {2025},
author = {Yau, R and Pavloudi, C and Zeng, Y and Saw, J and Eleftherianos, I},
title = {Infection with the entomopathogenic nematodes Steinernema alters the Drosophila melanogaster larval microbiome.},
journal = {PloS one},
volume = {20},
number = {5},
pages = {e0323657},
pmid = {40378358},
issn = {1932-6203},
mesh = {Animals ; *Drosophila melanogaster/microbiology/parasitology ; Larva/microbiology/parasitology ; *Microbiota ; *Rhabditida/physiology ; Xenorhabdus ; },
abstract = {The fruit fly Drosophila melanogaster is a vital model for studying the microbiome due to the availability of genetic resources and procedures. To understand better the importance of microbial composition in shaping immune modulation, we can investigate the role of the microbiota through parasitic infection. For this, we use entomopathogenic nematodes (EPN) of the genus Steinernema which exhibit remarkable ability to efficiently infect a diverse array of insect species, facilitated by the mutualistic bacteria Xenorhabdus found within their gut. To examine the microbiome changes in D. melanogaster larvae in response to Steinernema nematode infection, D. melanogaster late second to early third instar larvae were exposed separately to S. carpocapsae and S. hermaphroditum infective juveniles. We have found that S. carpocapsae infective juveniles are more pathogenic to D. melanogaster larvae compared to the closely related S. hermaphroditum. Our microbiome analysis also indicates substantial changes in the size and composition of the D. melanogaster larval microbiome during infection with either nematode species compared to the uninfected controls. Our results serve as a foundation for future studies to elucidate the entomopathogenic-specific effector molecules that alter the D. melanogaster microbiome and understand the role of the microbiome in regulating insect anti-nematode immune processes.},
}

Animals
*Drosophila melanogaster/microbiology/parasitology
Larva/microbiology/parasitology
*Microbiota
*Rhabditida/physiology
Xenorhabdus

@article {pmid40378286,
year = {2025},
author = {Fields, BD and Pascal, DG and Rando, OK and Huddleston, ME and Ingram, K and Hopton, R and Grogg, MW and Nelson, MT and Voigt, CA},
title = {Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00690},
pmid = {40378286},
issn = {2161-5063},
abstract = {Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (10[12] cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.},
}

@article {pmid40378154,
year = {2025},
author = {Goszcz, A and Furtak, K and Stasiuk, R and Wójtowicz, J and Musiałowski, M and Schiavon, M and Dębiec-Andrzejewska, K},
title = {Bacterial osmoprotectants - a way to survive in saline conditions and potential crop allies.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf020},
pmid = {40378154},
issn = {1574-6976},
abstract = {Soil salinization, affecting 6.5% of arable land, deteriorates soil properties, reduces microbiota activity, hinders plant growth, and accelerates soil erosion. Excessive salt induces physiological drought and toxicity stress in plants, causing chlorosis, ion imbalances, and enzyme disruptions. This paper discusses microorganisms' resistance mechanisms, plant responses to salt stress and summarizes current knowledge on bacterial osmoprotectants and their functions. It also reviews emerging agrobiotechnological strategies using microbial osmoprotectants to remediate salinized soils and enhance plant growth and productivity under salt stress. Osmoprotectants stabilize proteins, buffer redox potential, and retain water, thus alleviating osmotic stress and promoting bacteria and plants growth. Their application improves soil properties by enhancing aggregate formation, water permeability, moisture content, cation exchange capacity, and ion availability. Despite extensive literature on the function of osmoprotectants, the knowledge about their role in soil environments and agrobiotechnology applications remains limited. This paper indicates proposed research perspectives, including discovering new osmoprotectants, their correlation with soil fertilization, interactions with the soil microbiome, and plant responses. It also identifies significant knowledge gaps in these areas, highlighting the need for further studies to consolidate existing data and assess the potential of this approach to enhance soil health and crop productivity in saline environments.},
}

@article {pmid40377895,
year = {2025},
author = {Sharma, S and Kaur, I and Dubey, N and Goswami, N and Tanwar, SS},
title = {Berberine can be a Potential Therapeutic Agent in Treatment of Huntington's Disease: A Proposed Mechanistic Insight.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40377895},
issn = {1559-1182},
abstract = {Huntington's disease (HD) is a genetic neurodegenerative disorder caused by CAG repeat expansion in the HTT gene, producing mutant huntingtin (mHTT) protein. This leads to neuronal damage through protein aggregation, transcriptional dysregulation, excitotoxicity, and mitochondrial dysfunction. mHTT impairs protein clearance and alters gene expression, energy metabolism, and synaptic function. Therapeutic strategies include enhancing mHTT degradation, gene silencing via antisense oligonucleotides and RNAi, promoting neuroprotection through BDNF signaling, and modulating neurotransmitters like glutamate and dopamine. Berberine, a natural isoquinoline alkaloid, has emerged as a promising therapeutic option for HD due to its multifaceted neuroprotective properties. Research indicates that berberine can mitigate the progression of neurodegenerative diseases, including HD, by targeting various molecular pathways. It exhibits antioxidant, anti-inflammatory, and autophagy-enhancing effects, which are crucial in reducing neuronal damage and apoptosis associated with HD. These properties make berberine a potential candidate for therapeutic intervention in HD, as demonstrated in both cellular and animal models. Berberine activates the PI3K/Akt pathway, which is vital for cell survival and neuroprotection. It reduces oxidative stress and neuroinflammation, both of which are implicated in HD pathology. Berberine enhances autophagic processes, promoting the degradation of mutant huntingtin protein, a key pathological feature of HD. In transgenic HD mouse models, berberine administration has been shown to alleviate motor dysfunction and prolong survival. It effectively reduces the accumulation of mutant huntingtin in cultured cells, suggesting a direct impact on the disease's molecular underpinnings. Berberine's safety profile, established through its use in treating other conditions, supports its potential for clinical trials in HD patients. Its ability to modulate neurotransmitter levels and engage multiple signaling pathways further underscores its therapeutic promise. While berberine shows significant potential as a therapeutic agent for HD, further research is necessary to fully elucidate its mechanisms and optimize its clinical application. The current evidence in the review paper, primarily from preclinical studies, provides a strong foundation for future investigations into berberine's efficacy and safety in human HD patients.},
}

@article {pmid40377871,
year = {2025},
author = {Rahmati, R and Zarimeidani, F and Ghanbari Boroujeni, MR and Sadighbathi, S and Kashaniasl, Z and Saleh, M and Alipourfard, I},
title = {CRISPR-Assisted Probiotic and In Situ Engineering of Gut Microbiota: A Prospect to Modification of Metabolic Disorders.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377871},
issn = {1867-1314},
abstract = {The gut microbiota, a substantial group of microorganisms residing in the human body, profoundly impacts various physiological and pathological mechanisms. Recent studies have elucidated the association between gut dysbiosis and multiple organ diseases. Gut microbiota plays a crucial role in maintaining gastrointestinal stability, regulating the immune system and metabolic processes not only within the gastrointestinal tract but also in other organs such as the brain, lungs, and skin. Dysbiosis of the gut microbiota can disrupt biological functioning and contribute to the development of metabolic disorders. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated proteins (Cas) modules are adaptive immune systems in numerous archaea and bacteria. CRISPR/Cas is a versatile gene-editing tool that enables modification of the genome in live cells, including those within the gut microbiota. This technique has revolutionized gene editing due to its simplicity and effectiveness. It finds extensive applications in diverse scientific arenas, facilitating the functional screening of genomes during various biological processes. Additionally, CRISPR has been instrumental in creating model organisms and cell lines for research purposes and holds great potential for developing personalized medical treatments through precise genetic alterations. This review aims to explore and discuss the possibilities of CRISPR/Cas and the current trends in using this technique for editing gut microbiota genes in various metabolic disorders. By uncovering the valuable potential of CRISPR/Cas in modifying metabolic disorders through the human gut microbiota, we shed light on its promising applications.},
}

@article {pmid40377870,
year = {2025},
author = {Amen, RA and Hassan, YM and Essmat, RA and Ahmed, RH and Azab, MM and Shehata, NR and Elgazzar, MM and El-Sayed, WM},
title = {Harnessing the Microbiome: CRISPR-Based Gene Editing and Antimicrobial Peptides in Combating Antibiotic Resistance and Cancer.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40377870},
issn = {1867-1314},
abstract = {The growing crisis of antibiotic resistance and the increasing incidence of cancer have prompted the exploration of innovative approaches, such as gene editing and antimicrobial peptides (AMPs). The human microbiome is integral to various aspects of health, disease, and therapeutic development, influencing metabolic pathways, immune function, and pathogen resistance. Recent advances in gene editing technologies, particularly CRISPR (clustered regularly interspaced short palindromic repeats), have opened new avenues for leveraging the microbiome to address complex medical challenges, including combating multidrug-resistant pathogens and cancer. The microbiome plays a crucial role in combating antibiotic resistance by modulating microbial communities, influencing pathogen survival and susceptibility to treatments. This review explores the microbiome's dynamic role in metabolic regulation, its contribution to cancer management, and how AMPs help maintain homeostasis and exhibit emerging anticancer properties, supported by both preclinical findings and clinical evidence. Additionally, CRISPR-based microbiome engineering offers potential to enhance host-microbiome interactions, optimizing therapeutic outcomes. The integration of microbiome metagenomics and proteomics has led to the discovery of novel AMPs with targeted anticancer effects. Innovative strategies, such as engineered probiotics and CRISPR-based microbiome engineering, present exciting prospects for next-generation therapies. Despite these advances, the translation of microbiome-based therapies into clinical settings remains challenging due to ethical, regulatory, and ecological hurdles. This review underscores the transformative potential of microbiome-based interventions, emphasizing the role of personalized medicine in maximizing therapeutic efficacy. Furthermore, we also address critical research gaps, limitations, and future directions, including optimizing AMP stability, delivery, and bioavailability, as well as overcoming the regulatory and ethical challenges in clinical translation.},
}

@article {pmid40377699,
year = {2025},
author = {Cobos-Uribe, C and Dhingra, R and Almond, MA and Alexis, NE and Peden, DB and Roach, J and Rebuli, ME},
title = {Human Sputum Microbiome Composition and Sputum Inflammatory Cell Profiles Are Altered with Controlled Wood Smoke Exposure as a Model for Wildfire Smoke.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
pmid = {40377699},
issn = {1535-4970},
abstract = {RATIONALE: Wood smoke exposure is increasing worldwide due to the rise in wildfire events. Various studies have associated exposure to wildfire-derived smoke with adverse respiratory conditions. However, the mechanism by which this occurs is unknown. Previous studies using wood smoke as a model of wildfire smoke have focused on the respiratory immune response and have reported increased neutrophil percentage and cytokine production in airway samples. The effect of wood smoke on the respiratory microbiome, however, has not been examined.

METHODS: Healthy volunteers (N=54) were subjected to controlled wood smoke exposure (500 µg/m3) for two hours, and induced sputum samples were collected and processed for microbiome analysis, immune mediators, and cell differentials at baseline, six- and 24-hours post-exposure. A negative binomial mixed model analysis examined associations between microbiome components and inflammatory cells in sputum.

MAIN RESULTS: Following wood smoke exposure, while sputum microbiome diversity remained unchanged, the microbiome composition was altered, particularly the abundance of several low-abundance bacteria, including Fretibacterium and Selenomonas, indicating that this inhalational exposure can alter the composition of the sputum microbiome. Additionally, a significant decrease in macrophage cells was observed at 24 hours without a significant change in neutrophils. We further found small but significant associations between different taxa and macrophages (per mg of sputum), including a negative association with Fretibacterium.

CONCLUSIONS: Together, these findings demonstrate that inhalational wood smoke exposure can modify several low-abundance bacteria within the respiratory microbiome and that these changes are associated with sputum inflammatory cell alterations, providing insights for future studies to focus on respiratory innate immune host-microbiome crosstalk in the context of environmental exposures.},
}

@article {pmid40377649,
year = {2025},
author = {Turov F, O and Yatsyk S, P and Krapivkin A, I and Vrublevsky S, G and Mamedov I, S and Perevezentsev O, A},
title = {[Current understanding of the urinary tract microbiome in children].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {141-147},
pmid = {40377649},
issn = {1728-2985},
mesh = {Humans ; *Microbiota ; *Urinary Tract Infections/microbiology/drug therapy/diagnosis ; Child ; *Urinary Tract/microbiology ; Female ; Male ; },
abstract = {INTRODUCTION: The second most common reason for prescribing antibiotics in children is urinary tract infection (UTI). Since antimicrobial stewardship is a priority in the further development of strategies of the treatment of children with UTIs, the need to form an optimal model for its diagnosis and treatment is relevant in pediatric urology.

AIM: To analyze domestic and foreign publications devoted to the study of the urinary tract microbiome in children.

RESULTS: Cultivation or culturing methods continue to be considered the "gold standard" in many countries for the diagnosis of bacterial infections, although more sensitive and specific technologies are available. A urine sample was previously considered sterile if uropathogens did not grow using standard techniques. It remains unclear whether standard microbial culturing methods are adequate to determine species diversity and identify all microorganisms capable of causing UTIs. A study of the bladder microbiome and maintenance of its homeostasis to prevent inflammatory lower urinary tract diseases is an emerging area of research. It is known that the bladder of a healthy person contains non-uropathogenic bacteria, such as Lactobacillus, which are believed to function as an immune system and protect against the effects of uropathogens.},
}

Humans
*Microbiota
*Urinary Tract Infections/microbiology/drug therapy/diagnosis
Child
*Urinary Tract/microbiology
Female
Male

@article {pmid40377635,
year = {2025},
author = {Faniev M, V and Kadyrov Z, A and Druzhinina N, K and Stepanov V, S and Prokopiev Ya, V and Fedorenko T, V and Markelova M, I and Khusnutdinova D, R and Grigorieva T, V},
title = {[Characterization of the taxonomic structure of testicular and urethral microbiota in men with non-obstructive azoospermia with different outcomes in ART protocols].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {47-53},
pmid = {40377635},
issn = {1728-2985},
mesh = {Humans ; Male ; *Azoospermia/microbiology/therapy ; *Microbiota ; Adult ; *Testis/microbiology ; *Urethra/microbiology ; Retrospective Studies ; *Bacteria/classification/genetics/isolation & purification ; *Reproductive Techniques, Assisted ; RNA, Ribosomal, 16S/genetics ; },
abstract = {AIM: To carry out a comparative analysis of the taxonomic structure of the testicular and urethral microbiota of patients with non-obstructive azoospermia (NOA) in ART protocols with positive (live birth) and negative outcomes.

MATERIALS AND METHODS: The samples of testicular tissue and urethra of infertile patients with NOA (n=62) were evaluated. To realize the reproductive potential, all patients underwent micro-TESE in the ART protocol. All patients were retrospectively divided into two groups. In group 1, there were patients with NOA and a positive ART result (n=16), while in group 2 patients had NOA and a negative ART result (n=46). To study the bacterial diversity of testicular tissue, an analysis of amplicons of the bacterial 16S rRNA gene was performed using high-throughput NGS.

RESULTS: A comparative analysis of the relative representation of bacterial taxa in the testicular tissue of patients with NOA with positive and negative ART outcomes revealed a number of significant differences. For example, significant differences (p<0.05) were found in the relative representation of the phylum Fusobacteriota, the Pasteurellaceae, Dialisteraceae, Porphyromonadaceae, Alcanivoracaceae, Neisseriaceae_563222, Ruminococcaceae, Acutalibacteraceae, Peptostreptococcaceae_256921, Marinilabiliaceae, Exiguobacteraceae, Coprobacillaceae, Bacillaceae_H_289398, Burkholderiaceae_A_595427 in patients of group 1. Significant differences (p<0.05) were also found in the frequency of occurrence of the phylum Fusobacteriota, the families Lactobacillaceae, Pasteurellaceae, Alcanivoracaceae, Acutalibacteraceae, Peptostreptococcaceae_256921, Exiguobacteraceae, Coprobacillaceae, Bacillaceae_H_289398, Burkholderiaceae_A_595427 in patients with positive ART outcomes. When analyzing the urethral microbiome using high-throughput sequencing, no significant differences in alpha-diversity indices were shown. We also found significant differences (p<0.05) in the frequency of occurrence of the Streptococcaceae family, and they were more common in patients with negative ART outcomes. Meanwhile, representatives of the Enterococcaceae and Brevibacteriaceae families were more common in patients with positive ART outcomes.

CONCLUSIONS: It is obvious that changes in the microbiota of the genital tract have a specific effect on the reproductive system, and correction of abnormal microbiomes can improve reproductive outcomes.},
}

Humans
Male
*Azoospermia/microbiology/therapy
*Microbiota
Adult
*Testis/microbiology
*Urethra/microbiology
Retrospective Studies
*Bacteria/classification/genetics/isolation & purification
*Reproductive Techniques, Assisted
RNA, Ribosomal, 16S/genetics

@article {pmid40377498,
year = {2025},
author = {Angendohr, C and Koppe, C and Herebian, D and Schneider, AT and Keysberg, L and Singer, MT and Gilljam, J and Dille, MA and Bode, JG and Doll, S and Conrad, M and Vucur, M and Luedde, T},
title = {The ferroptosis mediator ACSL4 fails to prevent disease progression in mouse models of MASLD.},
journal = {Hepatology communications},
volume = {9},
number = {6},
pages = {},
doi = {10.1097/HC9.0000000000000684},
pmid = {40377498},
issn = {2471-254X},
mesh = {Animals ; *Ferroptosis/genetics ; *Coenzyme A Ligases/genetics/metabolism ; Disease Progression ; Mice ; Disease Models, Animal ; Mice, Knockout ; Diet, High-Fat/adverse effects ; *Fatty Liver/metabolism/etiology ; Male ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Long-Chain-Fatty-Acid-CoA Ligase ; Metabolic Syndrome ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is an increasingly prevalent condition and a major risk factor for chronic liver damage, potentially leading to steatohepatitis and HCC. It is already known that patients with MASLD show increased systemic and hepatic iron concentrations as well as perturbed lipid metabolism, suggesting the involvement of ferroptosis in the development and progression of MASLD. Consequently, inhibition of ferroptosis represents a potential therapeutic option for patients with MASLD.

METHODS: We investigated whether liver parenchymal cell-specific deletion (LPC-KO) of the pro-ferroptotic gene acyl-CoA synthetase long-chain family member 4 (ACSL4LPC-KO) reduces MASLD onset and progression in mice. ACSL4LPC-KO and wild-type littermates were fed a choline-deficient high-fat diet (CD-HFD) or a Western diet for 20 weeks (CD-HFD and Western diet) or 40 weeks (CD-HFD only) to monitor MASLD progression and metabolic syndrome development.

RESULTS: In contrast to the recently published studies by Duan et al, our results show no significant differences between ACSL4LPC-KO and wild-type mice with regard to the development of MASLD or the progression of metabolic syndrome. Furthermore, no differences were observed in metabolic parameters (ie, weight gain, glucose tolerance test, hepatic steatosis) or MASLD-associated inflammatory response.

CONCLUSIONS: Our analyses, therefore, suggest that loss of ACSL4 has no effect on the progression of MASLD induced by CD-HFD or the Western diet. The discrepancy between our and previously published results could be due to differences in the diets or the influence of a distinct microbiome, so the results obtained with hepatocyte-specific ACSL4LPC-KO should be taken with caution.},
}

Animals
*Ferroptosis/genetics
*Coenzyme A Ligases/genetics/metabolism
Disease Progression
Mice
Disease Models, Animal
Mice, Knockout
Diet, High-Fat/adverse effects
*Fatty Liver/metabolism/etiology
Male
Liver/metabolism/pathology
Mice, Inbred C57BL
Long-Chain-Fatty-Acid-CoA Ligase
Metabolic Syndrome

@article {pmid40377331,
year = {2025},
author = {Heil, JA and Bernardin, JR and Galla, SJ and Bittleston, LS},
title = {A framework for utilizing leaf-associated microbes to achieve conservation and restoration goals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0108224},
doi = {10.1128/msphere.01082-24},
pmid = {40377331},
issn = {2379-5042},
abstract = {Plant-associated microbiomes have profound effects on ecosystem functioning and play a role in the success of plants at both small and large scales. As key components of healthy plants and ecosystems, plant microbiomes should be considered in conservation and ecosystem management strategies. Many knowledge gaps and logistical barriers exist that increase the difficulty of employing microbes in conservation; however, some success has been achieved by manipulating the root microbiome and in agricultural contexts. In contrast with the root microbiome, the role of the leaf microbiome in conservation remains largely unexplored. In this perspective, we posit that the leaf microbiome plays an essential role in plant and ecosystem health and should be considered in conservation strategies. We include a framework for approaching leaf microbiome management, including identification of sources of disturbance, identifying mechanisms to address resulting plant stress, types of microbial inoculation to achieve desired outcomes, and co-producing plans of management with interest groups and rights holders.},
}

@article {pmid40377302,
year = {2025},
author = {Jourdain, L and Gu, W},
title = {Designing synthetic microbial communities for enhanced anaerobic waste treatment.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0040425},
doi = {10.1128/aem.00404-25},
pmid = {40377302},
issn = {1098-5336},
abstract = {Synthetic microbial communities (SynComs) are powerful tools for investigating microbial interactions and community assembly by focusing on minimal yet functionally representative members. Here, we will highlight key principles for designing SynComs, specifically emphasizing the anaerobic digestion (AD) microbiome for waste treatment and upcycling. The AD process has traditionally been used to reduce organic waste volume while producing biogas as a renewable energy source. Its microbiome features well-defined trophic layers and metabolic groups. There has been growing interest in repurposing the AD process to produce value-added products and chemical precursors, contributing to sustainable waste management and the goals of a circular economy. Optimizing the AD process requires a better understanding of microbial interactions and the influence of both biotic and abiotic parameters, where SynComs offer great promise. Focusing on AD microbiomes, we review the principles of SynComs' design, including keystone taxa and function, cross-feeding interactions, and metabolic redundancy, as well as how modeling approaches could guide SynComs design. Furthermore, we address practical considerations for working with AD SynComs and examine constructed SynComs designed for anaerobic waste digestion. Finally, we discuss the challenges associated with designing and applying SynComs to enhance our understanding of the AD process. This review aims to explore the use of synthetic communities in studying anaerobic digestion and highlights their potential for developing innovative biotechnological processes.},
}

@article {pmid40377187,
year = {2025},
author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM},
title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.89862},
pmid = {40377187},
issn = {2050-084X},
support = {1746045//National Science Foundation Graduate Research Fellowship Program/ ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM128716/NH/NIH HHS/United States ; RC2 DK122394/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Stress, Physiological ; Metagenome ; *Bacteria/metabolism/genetics/classification ; },
abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health vs IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Stress, Physiological
Metagenome
*Bacteria/metabolism/genetics/classification

@article {pmid40376856,
year = {2025},
author = {Takyi, E and Nirmalkar, K and Adams, J and Krajmalnik-Brown, R},
title = {Interventions targeting the gut microbiota and their possible effect on gastrointestinal and neurobehavioral symptoms in autism spectrum disorder.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2499580},
doi = {10.1080/19490976.2025.2499580},
pmid = {40376856},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Autism Spectrum Disorder/therapy/microbiology ; Probiotics/therapeutic use/administration & dosage ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Gastrointestinal Diseases/therapy/microbiology ; Gastrointestinal Tract/microbiology ; Child ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Autism spectrum disorder (ASD) is a developmental disorder that is characterized by deficits in social communication and restricted, repetitive, and stereotyped behaviors. In addition to neurobehavioral symptoms, children with ASD often have gastrointestinal symptoms (e.g. constipation, diarrhea, gas, abdominal pain, reflux). Several studies have proposed the role of gut microbiota and metabolic disorders in gastrointestinal symptoms and neurodevelopmental dysfunction in ASD patients; these results offer promising avenues for novel treatments of this disorder. Interventions targeting the gut microbiota - such as fecal microbiota transplant (FMT), microbiota transplant therapy (MTT), probiotics, prebiotics, synbiotics, antibiotics, antifungals, and diet - promise to improve gut health and can potentially improve neurological symptoms. The modulation of the gut microbiota using MTT in ASD has shown beneficial and long-term effects on GI symptoms and core symptoms of autism. Also, the modulation of the gut microbiota to resemble that of typically developing individuals seems to be the most promising intervention. As most of the studies carried out with MTT are open-label studies, more extensive double-blinded randomized control trials are needed to confirm the efficacy of MTT as a therapeutic option for ASD. This review examines the current clinical research evidence for the use of interventions that target the microbiome - such as antibiotics, antifungals, probiotics/prebiotics, synbiotics, and MTT - and their effectiveness in changing the gut microbiota and improving gastrointestinal and neurobehavioral symptoms in ASD.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Autism Spectrum Disorder/therapy/microbiology
Probiotics/therapeutic use/administration & dosage
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Gastrointestinal Diseases/therapy/microbiology
Gastrointestinal Tract/microbiology
Child
Anti-Bacterial Agents/therapeutic use

@article {pmid40376801,
year = {2025},
author = {Prisco, SZ and Blake, M and Kazmirczak, F and Moon, R and Kremer, BP and Hartweck, LM and Kim, M and Vogel, N and Mendelson, JB and Moutsoglou, D and Thenappan, T and Prins, KW},
title = {Lactobacillus Restructures the Micro/Mycobiome to Combat Inflammation-Mediated Right Ventricular Dysfunction in Pulmonary Arterial Hypertension.},
journal = {Circulation. Heart failure},
volume = {},
number = {},
pages = {e012524},
doi = {10.1161/CIRCHEARTFAILURE.124.012524},
pmid = {40376801},
issn = {1941-3297},
abstract = {BACKGROUND: Inflammation suppresses right ventricular (RV) function in pulmonary arterial hypertension (PAH). In particular, we showed GP130 (glycoprotein-130) signaling promotes pathological microtubule remodeling and RV dysfunction in rodent PAH. Emerging data demonstrate the intestinal microbiome regulates systemic inflammation, but the impact of modulating the gut microbiome on the GP130-microtubule axis in RV failure is unknown.

METHODS: Two weeks following monocrotaline injection, rats were administered daily Lactobacillus rhamnosus (4×10[7] colony-forming units) via oral gavage for 10 days. Next-generation metagenomics and internal transcribed spacer 2 sequencing delineated fecal bacterial and fungal compositions. SomaScan proteomics measured levels of 7596 serum proteins. RV immunoblots quantified protein abundances. Light or super resolution confocal microscopy assessed RV, lung, and jejunal morphology. Echocardiography and invasive closed-chest pressure-volume loops evaluated PAH severity and RV function. The relationship between Lactobacillus abundance and RV function was assessed in 65 patients with PAH.

RESULTS: Lactobacillus administration restructured both the intestinal micro- and mycobiome. The alteration in the gut ecosystem improved intestinal health as demonstrated by increased jejunal villus length and glycocalyx thickness and diminished intestinal permeability biomarkers. Serum proteomics revealed Lactobacillus modulated systemic inflammation and decreased circulating GP130 ligands. Lactobacillus-mediated suppression of GP130 signaling blunted pathological microtubule remodeling in RV cardiomyocytes. Microtubule-associated phenotypes, including RV cardiomyocyte and nuclear hypertrophy, transverse tubule integrity, and connexin-43 localization, were all corrected with Lactobacillus. These cellular changes manifested as improved RV function despite no significant alteration in PAH severity. Finally, patients with PAH and detectable fecal Lactobacillus had superior RV function despite similar mean pulmonary arterial pressure and pulmonary vascular resistance as compared with those without detectable Lactobacillus.

CONCLUSIONS: Lactobacillus supplementation restructures the gut micro/mycobiome, restores intestinal health, dampens systemic inflammation, and reduces GP130 ligands and associated RV cardiomyocyte microtubule remodeling. These data identify a novel microbiome-inflammation-microtubule axis that has therapeutic relevance for RV dysfunction.},
}

@article {pmid40376566,
year = {2025},
author = {},
title = {Correction to "Gut Microbiome and Metabolome Changes in Chronic Low Back Pain Patients With Vertebral Bone Marrow Lesions".},
journal = {JOR spine},
volume = {8},
number = {2},
pages = {e70074},
doi = {10.1002/jsp2.70074},
pmid = {40376566},
issn = {2572-1143},
abstract = {[This corrects the article DOI: 10.1002/jsp2.70042.].},
}

@article {pmid40376006,
year = {2025},
author = {Ma, J and Fang, Y and Li, S and Zeng, L and Chen, S and Li, Z and Ji, G and Yang, X and Wu, W},
title = {Interpretable machine learning algorithms reveal gut microbiome features associated with atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1528046},
pmid = {40376006},
issn = {1664-3224},
mesh = {*Dermatitis, Atopic/microbiology/diagnosis ; Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; Support Vector Machine ; },
abstract = {BACKGROUND: The "gut-skin axis" has been proposed to play an important role in the development and symptoms of atopic dermatitis. Therefore, we have constructed an interpretable machine learning framework to quantitatively screen key gut flora.

METHODS: The 16S rRNA dataset, after applying the centered log-ratio transformation, was analyzed using five different machine learning models: random forest, light gradient boosting machine, extreme gradient boosting, support vector machine with radial kernel, and logistic regression. Interpretable machine learning methods, such as SHAP values, were used to identify significant features associated with atopic dermatitis.

RESULTS: Random forest performed better than the other "tree" models in the validation partitions. The SHAP global dependency plot indicated that Bifidobacterium ranked as the strongest predictive factor across all prediction horizons, although the SHAP values for some features were still higher in support vector machine and logistic regression models. The SHAP partial dependency plot for "tree" models showed that the best segmentation point for Bifidobacterium was further from the origin compared to other features in the respective models, quantitatively reflecting differences in gut microbiota.

CONCLUSION: Machine learning models combined with SHAP could be used to quantitatively screen key gut flora in atopic dermatitis patients, providing doctors with an intuitive understanding of 16S rRNA sequencing data to support precision medicine in care and recovery.},
}

*Dermatitis, Atopic/microbiology/diagnosis
Humans
*Gastrointestinal Microbiome
*Machine Learning
RNA, Ribosomal, 16S/genetics
Algorithms
Support Vector Machine

@article {pmid40375898,
year = {2025},
author = {Xu, C and Zhao, LY and Ye, CS and Xu, KC and Xu, KY},
title = {The application of machine learning in clinical microbiology and infectious diseases.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1545646},
pmid = {40375898},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Communicable Diseases/diagnosis/microbiology ; *Microbiology ; Artificial Intelligence ; Algorithms ; },
abstract = {With the development of artificial intelligence(AI) in computer science and statistics, it has been further applied to the medical field. These applications include the management of infectious diseases, in which machine learning has created inroads in clinical microbiology, radiology, genomics, and the analysis of electronic health record data. Especially, the role of machine learning in microbiology has gradually become prominent, and it is used in etiological diagnosis, prediction of antibiotic resistance, association between human microbiome characteristics and complex host diseases, prognosis judgment, and prevention and control of infectious diseases. Machine learning in the field of microbiology mainly adopts supervised learning and unsupervised learning, involving algorithms from classification and regression to clustering and dimensionality reduction. This Review explains crucial concepts in machine learning for unfamiliar readers, describes machine learning's current applications in clinical microbiology and infectious diseases, and summarizes important approaches clinicians must be aware of when evaluating research using machine learning.},
}

Humans
*Machine Learning
*Communicable Diseases/diagnosis/microbiology
*Microbiology
Artificial Intelligence
Algorithms

@article {pmid40375894,
year = {2025},
author = {Li, Q and Zhang, Y and Wang, X and Dai, L and Zhao, W},
title = {Gut microbiota of patients with post-stroke depression in Chinese population: a systematic review and meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1444793},
pmid = {40375894},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Stroke/complications/microbiology ; *Depression/microbiology/etiology ; China/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; Asian People ; East Asian People ; },
abstract = {BACKGROUND: Evidence of changes in the composition and function of the gut microbiota (GM) in post-stroke depression (PSD) patients is gradually accumulating. This study aimed to systematically evaluate the relationship between PSD and GM.

METHODS: We searched in PubMed, Web of Science, Embase, Cochrane databases, Wangfang, VIP, CBM, and CNKI from the establishment of the database to April 17, 2024, and systematic review and meta-analysis were performed to investigate the differences of GM between patients with PSD spectrum and healthy controls (HC) or stroke spectrum.

RESULT: There were 14 studies consisting a total of 1,556 individuals included in the meta-analysis. The pooled results showed that PSD spectrum demonstrated significantly increased α diversity as indexed by Chao1 index, ACE indexes, Shannon index, and Simpson index as compared to HC. Additionally, stroke spectrum significantly increased α diversity as indexed by Simpson index compared to PSD. Furthermore, the pooled estimation of relative abundance showed that Bacteroidota, Fusobacteriota, and Pseudomonadota in PSD patients were significantly higher than those in the HC group, while the abundance of Bacillota was higher in the HC group. Moreover, significant differences in GM were observed between PSD patients and HC at the family and genus levels.

CONCLUSION: This study found that the α diversity of PSD patients was higher than that of HC. Moreover, there were also differences in the distribution of GM at the phylum, family, and genus levels, respectively. At the same time, the level of Lachnospira in PSD patients was lower than that in the stroke group.

https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42024582708.},
}

Humans
*Gastrointestinal Microbiome
*Stroke/complications/microbiology
*Depression/microbiology/etiology
China/epidemiology
*Bacteria/classification/genetics/isolation & purification
Asian People
East Asian People

@article {pmid40375709,
year = {2025},
author = {Kumar, A and Bawa, Y and Pramanik, J and Batta, K and Prajapati, B and Mehra, R and Menkinoska, M and Petkoska, AT},
title = {Unveiling the Role and Mechanism of Mycoprotein for Reducing Cardiovascular Risk.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010347951250416140136},
pmid = {40375709},
issn = {1873-4316},
abstract = {Cardiovascular diseases (CVDs) have the highest mortality rates worldwide. To reduce the risk of CVDs, dietary interventions are a potential approach. This review explores the potential of mycoprotein, a fungal-derived protein, as a dietary approach for maintaining cardiovascular health. A comprehensive literature search was conducted using various databases (Web of Science, Medline, Scopus, Google Scholar, EBSCO, PubMed) and government websites (WHO, CDC) to identify relevant studies. Mycoprotein provides essential amino acids with high bioavailability (0.996) while containing minimal saturated fat (1.5 grams) and high fiber (6 grams). Clinical studies have shown that mycoprotein consumption reduces cholesterol, improves lipid profiles, and potentially lowers blood pressure, possibly due to its impact on gut microbiota (GM) and short-chain fatty acids (SCFAs) production. The intestinal fermentation of mycoprotein fiber increases the abundance of beneficial gut bacteria, binds to Gprotein coupled receptors like GPR41 and 43 to promote vasodilation, inhibits the angiotensinconverting enzyme, and reduces hepatic cholesterol production. Chitin and beta-glucan, the primary fiber of mycoprotein, exhibit anti-inflammatory properties that may contribute to overall cardiovascular health. The study concludes that mycoprotein is a sustainable and nutritious alternative, and its consumption promotes cardiovascular health and reduces CVD risks.},
}

@article {pmid40375701,
year = {2025},
author = {Tiwari, R and Tiwari, G and Singh, A and Dhas, N},
title = {Pharmacological Foundation and Novel Insights of Resveratrol in Cardiovascular System: A Review.},
journal = {Current cardiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/011573403X343252250502045328},
pmid = {40375701},
issn = {1875-6557},
abstract = {Research into drugs that can enhance cardiovascular health has been sparked by the rising prevalence of cardiovascular illnesses (CVDs). In addition to its anti-inflammatory and antioxidant qualities, Resveratrol (RES) is well known for its capacity to increase endothelial NO synthase (eNOS) activity. This page summarises RES's wide effects on energy metabolism, resilience to stress, exercise mimicking, circadian rhythm, lifespan control, and microbiome composition. This article addresses the poor and contradictory results shown in preclinical and clinical trials provides an update on the cardiovascular preventive properties of RES. The activation of AMP-activated protein kinase (AMPK), silent information regulator 1 (SIRT1), and natural antioxidant enzymes is associated with some of the positive effects of RES on the cardiovascular system. A microarray data summary indicates a strong correlation between the heart's reaction to calorie restriction and the transcriptional responses to RES. RES has been demonstrated to reduce contractile dysfunction, cardiac remodelling, and hypertrophy in several animal models of heart failure. Its preventive properties are believed to be due to several molecular pathways, including the suppression of prohypertrophic signalling molecules, enhancement of cardiac Ca2+ handling, control of autophagy, and decreases in inflammation. RES thus has the potential to be used in several novel therapeutic approaches for treating diseases such as atherosclerosis, ischemia/reperfusion damage, metabolic syndrome, heart failure, and inflammatory changes associated with ageing.},
}

@article {pmid40375477,
year = {2025},
author = {Hagel, JM and Chang, L and Li, J and Chen, X and Yu, L and Gallant, JA and Facchini, PJ},
title = {Bioproduction of a Large-Scale Library of Tryptamine Derivatives for Neuropsychiatric Drug Screening.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.4c00857},
pmid = {40375477},
issn = {1554-8937},
abstract = {Drug screening programs targeting novel indolethylamines with pharmacological properties suitable for the treatment of psychiatric and central nervous system disorders benefit from the availability of large compound libraries normally prepared using synthetic chemistry. Bioproduction strategies based on microbial metabolic engineering and fermentation generally fail to achieve the throughput, scale, or versatility of synthetic chemistry owing, in part, to a lack of efficient and promiscuous enzymes. Moreover, synthetic biology rarely extends to the purification of targeted products, which is an essential component of synthetic chemistry and drug screening regimes. A lattice of biosynthetic routes beginning with endogenous tryptophan or exogenous indole derivatives were engineered in Escherichia coli using heterologous genes encoding enzymes sourced from plants, mushrooms, microbes and animals. Twelve tryptophan decarboxylase candidates were screened and highly versatile top-performers from Bacillus atrophaeus and the gut microbiome species Clostridium sporogenes were identified. Seven halogenases, three tryptophan synthase β-subunits, six N-methyltransferases, five regioselective prenyltransferases, a cytochrome P450 oxidoreductase 5-hydroxylase, an N-acetyltransferase, a 4-O-kinase and various accessory proteins were also tested. These enzymes were used in various combinations and permutations to build E. coli strains capable of 344 putative biotransformations, which resulted in the formation of 279 products with only 63 targeted compounds not detected. A set of 17 novel N-acetylated derivatives were selected for upscaled culturing and purification to ≥95% from 0.5 to 1 L of the fermentation broth, which yielded ∼6-80 mg of each molecule. The potential of each compound for bioactivity at 14 different receptors or transporters with established or purported involvement in neuropsychiatric diseases was tested using a single ligand concentration. Nearly all the N-acetylated compounds showed interaction with the melatonin (MT1) receptor, and several molecules showed interaction with serotonergic receptors 5-HT2B, 5-HT2C, and 5-HT7. Overall, we show that bio-fermentation is useful in the large-scale screening of molecules with potential in drug development.},
}