@article {pmid40288425,
year = {2025},
author = {Hu, J and Liu, J and Wu, H and Zhao, T and Li, Z and Luo, J},
title = {Differences in the gut and pharyngeal microbiomes before and after treatment of an acute exacerbation of chronic obstructive pulmonary disease.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107635},
doi = {10.1016/j.micpath.2025.107635},
pmid = {40288425},
issn = {1096-1208},
abstract = {This study investigated the gut microbiota and pharyngeal microbiome before and after treatment of an acute exacerbation of chronic obstructive pulmonary disease (AECOPD). The abundance and diversity of microorganisms in the gut and pharynx were examined in 24 patients before and after treatment of AECOPD. Enzyme-linked immunosorbent assay was used to detect inflammatory factors in venous blood and 16S rDNA sequencing was performed. The concentration of short-chain fatty acids (SCFAs) in fecal samples was measured by chromatography-mass spectrometry. The results indicated that the diversity and richness of the gut microbiota decreased post-treatment. The linear discriminant analysis effect size (LEfSe) algorithm revealed an increase in the abundance of f_Dietziaceae, g_Dietzia, g_Megasphaera, g_Robinsoniella, s_Salivarius, and s_Peoriensis in the gut after treatment. There was also a post-treatment decrease in the richness of the pharyngeal microbiome. LEfSe revealed a high abundance of p_Actinobacteria, f_Bacteriodaceae, o_Thermales, g_Bacteroides, and g_Thermus in the pharynx before treatment, and an increased abundance of o_Enterobacterales, f_Enterobacteriaceae, f_Ruminococcaceae, and g_Faecalibacterium after treatment. There were no post-treatment changes in SCFA levels. However, the serum C-reactive protein level decreased after treatment. Levels of other inflammatory factors, including tumor necrosis factor-alpha, interleukin (IL)-1β, IL-6, IL-10, transforming growth factor-beta, IL-23, IL-17, and interferon-gamma, were consistent before and after treatment. In this study, changes in the gut microbiota and pharyngeal microbiome occurred after treatment for AECOPD, with no changes in levels of SCFAs or inflammatory factors, except for a decrease in the C-reactive protein level.},
}

@article {pmid40288073,
year = {2025},
author = {Song, Y and Baniakina, LFT and Jiang, L and Chai, L},
title = {Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {55},
number = {},
pages = {101522},
doi = {10.1016/j.cbd.2025.101522},
pmid = {40288073},
issn = {1878-0407},
abstract = {Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.},
}

@article {pmid40287991,
year = {2025},
author = {Hui, D and Pan, L},
title = {Hybrid Neural network and machine learning models with improved optimization method for gut microbiome effects on the sleep quality in patients with endometriosis.},
journal = {Computer methods and programs in biomedicine},
volume = {267},
number = {},
pages = {108776},
doi = {10.1016/j.cmpb.2025.108776},
pmid = {40287991},
issn = {1872-7565},
abstract = {BACKGROUND AND OBJECTIVE: Endometriosis is a chronic gynecological condition known to affect the quality of life of millions of women globally, often manifesting with symptoms that impact sleep quality. Emerging evidence suggests a crucial role of the gut microbiome in regulating various physiological processes, including sleep. This study investigates the relationship between gut microbiome composition and sleep quality in patients with endometriosis using machine learning (ML) techniques named artificial neural network (ANN) and support vector regression (SVR) with several hybrid approaches as ML-based ANN and SVR coupled with optimization using partial swarm optimization (PSO) and an improved PSO. We analyzed data from 200 endometriosis patients, encompassing a diverse range of age, Body mass index (BMI), symptom severity, and lifestyle factors. Key gut microbiota, including Bacteroides, Prevotella, Ruminococcus, Lactobacillus, Faecalibacterium, and Akkermansia, were quantified. Additionally, lifestyle variables such as diet quality, physical activity level, daily caloric intake, fiber intake, sugar intake, alcohol consumption, smothking status are applied for predictions of sleep quality.

METHODS: Advanced machine learning models, including Support Vector Machines (SVM), Neural Networks (NN) were employed to analyze the data. Two hybrid machine learning method named SVM- improved particle swarm optimization (IPSO) and NN-IPSO as hybrid SVR and NN combined with an IPSO is proposed for prediction of sleep quality. In the enhanced PSO, a local search position of particle is developed for better calibration of the parameters in NN and SVM applied in hybrid models. In local search of improved PSO, the best particle is applied with a random adjusting process applied for new particles.

RESULTS AND CONCLUSION: These several ML methods showed that revealed significant associations between specific gut microbiota and sleep quality in endometriosis patients. The hybrid methods are more accurate than traditional machine learning methods-based NN and SVR that these methods exhibit a strong predictive tendency by using the local search. Exploring the underlying mechanisms through which the gut microbiome influences sleep could provide deeper insights into potential therapeutic targets.},
}

@article {pmid40287964,
year = {2025},
author = {Lu, Y and Xu, L and Chen, W and Liu, W and Zhang, Y and Zhou, Q and Wang, N and Zhang, Y and Bai, H and Xu, S and Huang, P and Fu, K and Xie, W and Liu, X and Wang, X and Wong, CC and Kuang, M and Yu, J},
title = {Intra-hepatic microbial heterogeneity in multifocal hepatocellular carcinoma and its association with host genomic and transcriptomic alterations.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-24-1259},
pmid = {40287964},
issn = {2159-8290},
abstract = {The signature of intrahepatic microbiome in multifocal hepatocellular carcinoma (HCC) and its association with genomic alterations remain elusive. Here, we performed multi-omics profiling of 242 HCC tumor nodules and 58 adjacent non-tumor tissues from 58 multifocal HCC patients, revealing heterogeneous microbial communities in multifocal HCC. Presence of bacteria in HCC nodules was confirmed by gram-stain, LPS, LTA staining and TEM. Mutational profiling stratified patients into intrahepatic metastasis (IM)-HCC and multicentric occurrence (MO)-HCC. Bacterial communities differed between IM and MO nodules (P=0.01). A 9-bacteria biomarker panel could distinguish IM nodules from MO nodules with AUROC of 0.795. Epithelial-mesenchymal transition (EMT) pathway was up-regulated in IM nodules and correlated with IM-enriched bacteria. IM-enriched bacteria such as Enterococcus faecalis and Streptococcus anginosus promoted HCC cell migration and invasion, and tumor progression in orthotopic HCC mouse models by inducing immunosuppressive microenvironment and EMT. Collectively, intrahepatic microbiome contributes to heterogeneity and pathogenesis of multifocal HCC.},
}

@article {pmid40287897,
year = {2025},
author = {Ombura, FLO and Malele, I and Abd-Alla, AM and Akutse, KS and Ajene, IJ and Khamis, FM},
title = {Potential of entomopathogenic fungi for Glossina austeni control: insights into microbiome alterations and implications on sustainable management of the pest.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70052},
pmid = {40287897},
issn = {1744-7917},
support = {D42017//International Atomic Energy Agency/ ; },
abstract = {Glossina austeni Newstead (Diptera: Glossinidae) is a competent vector of the trypanosomes causing human African trypanosomiasis and the African animal trypanosomosis. Management of this pest has primarily involved trapping methods, Sterile Insect Technique, and research into vector competence-symbiotic interactions. Nevertheless, the use of entomopathogenic fungi (EPF) in integrated pest management programs for G. austeni control remains limited. Moreover, different tsetse fly species exhibit varying susceptibility to different EPF strains, indicating that no single strain is universally effective. Therefore, our study aimed to identify candidate EPF isolates for G. austeni management, evaluate the effects of temperature on the radial growth of these potent isolates, and assess the impact of the candidate EPF on the gut microbiome of G. austeni. Consequently, 16 Metarhizium anisopliae (Metschn.) Sorokin isolates were screened against G. austeni using dry conidia in an infection chamber, with the most virulent isolates having LT50 values of 3.95-9.37 d. Temperature significantly influenced the radial growth, conidia germination, and yield of these strains. There were also significant differences in conidia acquisition, retention and transmission between male and female G. austeni flies. Furthermore, all conidia receivers carried sufficient conidia, 5 d post-interaction with EPF-challenged conidia donors. Microbiome analysis revealed Wigglesworthia, Serratia, Klebsiella, and Escherichia as the most abundant taxa. Among the M. anisopliae isolates, ICIPE 82 exhibited the fastest radial growth and highest thermostability, hence selected as a potential biopesticide candidate for managing G. austeni. This study demonstrates the efficacy and potential of M. anisopliae ICIPE 82 as a biopesticide for controlling G. austeni.},
}

@article {pmid40287860,
year = {2025},
author = {Li, Y and Liu, C and Wang, Y and Li, M and Zou, S and Hu, X and Chen, Z and Li, M and Ma, C and Obi, CJ and Zhou, X and Zou, Y and Tang, M},
title = {Urban wild bee well-being revealed by gut metagenome data: A mason bee model.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70051},
pmid = {40287860},
issn = {1744-7917},
support = {//Research Development Fund, Xi'an Jiaotong-Liverpool University/ ; //Summer Undergraduate Research Fellowship (SURF) Programme, Xi'an Jiaotong-Liverpool University/ ; },
abstract = {Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.},
}

@article {pmid40287826,
year = {2025},
author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Jain, C and Tiedje, JM and Cole, JR and Konstantinidis, KT},
title = {FastAAI: efficient estimation of genome average amino acid identity and phylum-level relationships using tetramers of universal proteins.},
journal = {Nucleic acids research},
volume = {53},
number = {8},
pages = {},
doi = {10.1093/nar/gkaf348},
pmid = {40287826},
issn = {1362-4962},
support = {DBI1356288NSF//NSF/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Software ; *Bacteria/genetics/classification ; *Amino Acids/genetics ; *Computational Biology/methods ; },
abstract = {Estimation of whole-genome relatedness and taxonomic identification are two important bioinformatics tasks in describing environmental or clinical microbiomes. The genome-aggregate Average Nucleotide Identity is routinely used to derive the relatedness of closely related (species level) microbial and viral genomes, but it is not appropriate for more divergent genomes. Average Amino-acid Identity (AAI) can be used in the latter cases, but no current AAI implementation can efficiently compare thousands of genomes. Here we present FastAAI, a tool that estimates whole-genome pairwise relatedness using shared tetramers of universal proteins in a matter of microseconds, providing a speedup of up to 5 orders of magnitude when compared with current methods for calculating AAI or alternative whole-genome metrics. Further, FastAAI resolves distantly related genomes related at the phylum level with comparable accuracy to the phylogeny of ribosomal RNA genes, substantially improving on a known limitation of current AAI implementations. Our analysis of the resulting AAI matrices also indicated that bacterial lineages predominantly evolve gradually, rather than showing bursts of diversification, and that AAI thresholds to define classes, orders, and families are generally elusive. Therefore, FastAAI uniquely expands the toolbox for microbiome analysis and allows it to scale to millions of genomes.},
}

Phylogeny
*Genome, Bacterial
*Software
*Bacteria/genetics/classification
*Amino Acids/genetics
*Computational Biology/methods

@article {pmid40287811,
year = {2025},
author = {Yuan, L and Luan, Y and Hong, W and Zhang, B and Xiong, Y},
title = {Effects of Aerobic Exercise and Intermittent Fasting on Fecal Microbiome Diversity in Obese Mice.},
journal = {Discovery medicine},
volume = {37},
number = {195},
pages = {765-771},
doi = {10.24976/Discov.Med.202537195.66},
pmid = {40287811},
issn = {1944-7930},
mesh = {Animals ; *Physical Conditioning, Animal ; *Fasting/physiology ; *Feces/microbiology ; Mice ; *Obesity/microbiology ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Male ; Mice, Obese ; Mice, Inbred C57BL ; Intermittent Fasting ; },
abstract = {BACKGROUND: Obesity threatens human health, and interventions to reduce obesity may have important effects on the gut microbiota. This study investigated alterations in gut microbial composition in response to aerobic exercise (AE) and intermittent fasting (IF).

METHODS: We randomly divided mice into four groups of seven mice each: normal, obesity, exercise, and fasting. The normal group was fed a Chow Diet, whereas the other three groups were fed a High Fat Diet (HFD). After 13 weeks, the exercise group was subjected to aerobic treadmill running, and the fasting group started IF for 8 weeks. We then analyzed the composition of the fecal microbiome in all mice at the end of 21 weeks.

RESULTS: Our investigation revealed that the HFD significantly influenced species (s)_Romboutsia ilealis, genus (g)_Dubosiella, and g_Blautia. AE predominantly affected family (f)_Rhizobiaceae and g_Rikenella, indicating its impact on enhancing microbial taxa associated with improved metabolic health profiles. On the other hand, IF prominently altered the abundance of s_Lactobacillus johnsonii and g_Colidextribacter, which are known for their roles in enhancing glucolipid metabolism and anti-inflammatory activity. Furthermore, the exercise group displayed increased diversity within f_Rhizobiaceae, potentially associated with anti-inflammatory benefits. The IF intervention was particularly effective in enriching s_Lactobacillus johnsonii, suggesting its pivotal role in regulating metabolic responses influenced by fasting.

CONCLUSION: The results demonstrated significant beneficial alterations in microbial composition following AE and IF interventions, which supports the use of personalized approaches for obesity management and overall health.},
}

Animals
*Physical Conditioning, Animal
*Fasting/physiology
*Feces/microbiology
Mice
*Obesity/microbiology
Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome
Male
Mice, Obese
Mice, Inbred C57BL
Intermittent Fasting

@article {pmid40287783,
year = {2025},
author = {Fan, Y and Li, Y and Gu, X and Chen, N and Chen, Y and Fang, C and Wang, Z and Yin, Y and Deng, H and Dai, L},
title = {Intestinal metabolites in colitis-associated carcinogenesis: Building a bridge between host and microbiome.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40287783},
issn = {2542-5641},
abstract = {Microbial-derived metabolites are important mediators of host-microbial interactions. In recent years, the role of intestinal microbial metabolites in colorectal cancer has attracted considerable attention. These metabolites, which can be derived from bacterial metabolism of dietary substrates, modification of host molecules such as bile acids, or directly from bacteria, strongly influence the progression of colitis-associated cancer (CAC) by regulating inflammation and immune response. Here, we review how microbiome metabolites short-chain fatty acids (SCFAs), secondary bile acids, polyamines, microbial tryptophan metabolites, and polyphenols are involved in the tumorigenesis and development of CAC through inflammation and immunity. Given the heated debate on the metabolites of microbiota in maintaining gut homeostasis, serving as tumor molecular markers, and affecting the efficacy of immune checkpoint inhibitors in recent years, strategies for the prevention and treatment of CAC by targeting intestinal microbial metabolites are also discussed in this review.},
}

@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}

*Rhizosphere
*Metagenomics/methods
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Glycine max/microbiology/growth & development
*Microbiota/genetics
China
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40287669,
year = {2025},
author = {Wallis, C and Ellerby, Z and Amos, G and Holcombe, LJ},
title = {Influence of wet and dry commercial diets on the oral microbiota of Yorkshire terriers.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {290},
pmid = {40287669},
issn = {1746-6148},
support = {N/A//Mars Petcare/ ; N/A//Mars Petcare/ ; N/A//Mars Petcare/ ; N/A//Mars Petcare/ ; },
mesh = {Animals ; Dogs/microbiology ; *Dental Plaque/microbiology/veterinary ; *Diet/veterinary ; *Animal Feed/analysis ; *Microbiota ; Male ; Female ; Periodontal Diseases/veterinary/prevention & control/microbiology ; Dog Diseases/microbiology/prevention & control ; *Mouth/microbiology ; Bacteria/classification/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Periodontal disease is common in dogs and is initiated by the build-up of plaque on the tooth surface. There is evidence that the feeding of dry diets may help prevent the build-up of plaque and calculus compared to softer wet diets. The primary objective of this study was to determine whether diet format influences the microbial composition of dental plaque.

RESULTS: Subgingival (SG) and gingival margin (GM) plaque samples were collected from 28 Yorkshire terriers, housed within a research facility, between 37 and 53 weeks of age. Dogs were fed either wet commercial diets, dry commercial diets, or a simultaneous offering of the two. Illumina sequencing of the 16 S rRNA gene (variable regions 3 and 4) of 43 SG and 43 GM plaque samples resulted in the generation of 6,725,682 paired end reads. Exploratory factor analysis, a statistical method for dimensionality reduction of multivariate data, was used to identify groups of covarying bacterial species. Subsequent mixed effects modelling revealed significant differences in the scores of two of these groupings indicating systematic differences in prevalences of their component taxa. One grouping revealed that for GM plaque samples, the profile of bacterial species most descriptive of the wet diet was biased towards those associated with periodontal disease whereas for the dry diet it was biased towards those associated with healthy gingiva. The dogs fed a mixture of wet and dry diets had bacterial profiles in between the wet and dry diets, i.e. a mix of both health and disease associated taxa. The other bacterial grouping indicated that, in dogs fed a wet diet only, GM plaque was significantly associated with bacteria that preferred aerobic conditions whereas SG plaque was associated with taxa that favoured anaerobic conditions.

CONCLUSIONS: Although dry diets shifted the bacterial community towards a healthier profile compared to wet diets there was no evidence of improved periodontal health. Additional methods to maintain dental hygiene should therefore be promoted to ensure effective management of periodontal disease in dogs.},
}

Animals
Dogs/microbiology
*Dental Plaque/microbiology/veterinary
*Diet/veterinary
*Animal Feed/analysis
*Microbiota
Male
Female
Periodontal Diseases/veterinary/prevention & control/microbiology
Dog Diseases/microbiology/prevention & control
*Mouth/microbiology
Bacteria/classification/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid40287646,
year = {2025},
author = {He, L and Zou, Q and Wang, Y},
title = {metaTP: a meta-transcriptome data analysis pipeline with integrated automated workflows.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {111},
pmid = {40287646},
issn = {1471-2105},
support = {62102269//National Natural Science Foundation of China/ ; },
mesh = {Workflow ; *Software ; *Gene Expression Profiling/methods ; *Computational Biology/methods ; *Transcriptome ; Microbiota/genetics ; Humans ; },
abstract = {BACKGROUND: The accessibility of sequencing technologies has enabled meta-transcriptomic studies to provide a deeper understanding of microbial ecology at the transcriptional level. Analyzing omics data involves multiple steps that require the use of various bioinformatics tools. With the increasing availability of public microbiome datasets, conducting meta-analyses can reveal new insights into microbiome activity. However, the reproducibility of data is often compromised due to variations in processing methods for sample omics data. Therefore, it is essential to develop efficient analytical workflows that ensure repeatability, reproducibility, and the traceability of results in microbiome research.

RESULTS: We developed metaTP, a pipeline that integrates bioinformatics tools for analyzing meta-transcriptomic data comprehensively. The pipeline includes quality control, non-coding RNA removal, transcript expression quantification, differential gene expression analysis, functional annotation, and co-expression network analysis. To quantify mRNA expression, we rely on reference indexes built using protein-coding sequences, which help overcome the limitations of database analysis. Additionally, metaTP provides a function for calculating the topological properties of gene co-expression networks, offering an intuitive explanation for correlated gene sets in high-dimensional datasets. The use of metaTP is anticipated to support researchers in addressing microbiota-related biological inquiries and improving the accessibility and interpretation of microbiota RNA-Seq data.

CONCLUSIONS: We have created a conda package to integrate the tools into our pipeline, making it a flexible and versatile tool for handling meta-transcriptomic sequencing data. The metaTP pipeline is freely available at: https://github.com/nanbei45/metaTP .},
}

Workflow
*Software
*Gene Expression Profiling/methods
*Computational Biology/methods
*Transcriptome
Microbiota/genetics
Humans

@article {pmid40287436,
year = {2025},
author = {Nørstebø, SF and Rodriguez-Campos, S and Umu, ÖCO and Abril-Parreño, L and Dalland, M and Gilfillan, GD and Fair, S and Krogenaes, A},
title = {The cervical microbiome of ewe breeds with known divergent fertility following artificial insemination with frozen-thawed semen.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14614},
pmid = {40287436},
issn = {2045-2322},
support = {SusAN;Grant no. 16/RD/SusAn/ERA-NET//European Research Area Network on Sustainable Animal Production/ ; NFR 272338 / E50//Norges Forskningsråd/ ; },
mesh = {Animals ; Female ; *Insemination, Artificial/veterinary ; Sheep/microbiology ; *Fertility ; *Cervix Uteri/microbiology ; *Microbiota ; Male ; *Semen/microbiology ; Cryopreservation ; Pregnancy ; *Semen Preservation/veterinary ; },
abstract = {The use of artificial insemination (AI) with frozen-thawed semen in sheep is limited internationally due to low pregnancy rates. An exception is Norway, where high success rates routinely occur following vaginal deposition of frozen-thawed semen during natural estrus. Previous research suggests that breed-specific differences in pregnancy rates may result from impaired cervical sperm transport. This study compared cervical microbiomes among sheep breeds with known differences in pregnancy rates after AI. Cervical samples were collected from Suffolk (low fertility) and Belclare (medium fertility) breeds in Ireland, and Norwegian white sheep (NWS) and Fur breeds (both high fertility) in Norway, during the follicular phase of both natural and synchronized estruses, and the luteal phase of synchronized estrus. Amplicon sequencing revealed significantly higher bacterial abundance during the follicular phase in the low-fertility Suffolk breed compared to high-fertility breeds. Alpha diversity was higher in Suffolk and Belclare breeds, especially during the natural follicular phase, coinciding with pronounced beta diversity differences among breeds. Genus Histophilus was the top feature leading to microbial differences between ewe breeds and types of cycle. Ewe breed was the main driver of cervical microbial composition; increased microbial load in lower-fertility breeds may negatively impact sperm survival/transport, hampering AI success.},
}

Animals
Female
*Insemination, Artificial/veterinary
Sheep/microbiology
*Fertility
*Cervix Uteri/microbiology
*Microbiota
Male
*Semen/microbiology
Cryopreservation
Pregnancy
*Semen Preservation/veterinary

@article {pmid40287413,
year = {2025},
author = {Saidi, F and Graybill, LA and Tang, JH and Phanga, T and Milala, B and Banda, G and Kamija, M and Kasaro, M and Mutale, W and Price, J and Chinula, L and Stringer, J and Hosseinipour, MC and Chi, BH and Ravel, J and Holm, JB},
title = {Effect of initiation of antiretroviral drugs for HIV prevention or treatment on the vaginal microbiome of pregnant women in Malawi.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {67},
pmid = {40287413},
issn = {2055-5008},
support = {P30AI50410//University of North Carolina at Chapel Hill Center for AIDS Research/ ; D43TW009340, D43 TW010060/TW/FIC NIH HHS/United States ; R01AI131060//US National Institute of Allergies and Infectious Diseases/ ; R01AI131060//US National Institute of Allergies and Infectious Diseases/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; OPP1033514//Bill and Melinda Gates Foundation/ ; },
mesh = {Humans ; Female ; Pregnancy ; Malawi ; *HIV Infections/prevention & control/drug therapy/microbiology ; *Vagina/microbiology ; Adult ; *Microbiota/drug effects ; *Pregnancy Complications, Infectious/drug therapy/prevention & control/microbiology ; Pre-Exposure Prophylaxis ; Young Adult ; *Anti-HIV Agents/therapeutic use ; Premature Birth ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Anti-Retroviral Agents/therapeutic use ; Pregnant People ; },
abstract = {Lack of Lactobacillus and/or dysbiosis is linked to spontaneous preterm birth (sPTB). The impact of antiretrovirals (ARVs) for HIV treatment or prevention on the vaginal microbiome during pregnancy remains unclear. We examined vaginal microbiome changes in pregnant women in Lilongwe, Malawi. Women living with HIV (WLHIV) initiated antiretroviral therapy (ART), while HIV-negative women began oral pre-exposure prophylaxis (PrEP). Of 255 participants (191 HIV-negative, 64 WLHIV) who provided baseline vaginal swabs, 181 provided follow-up swabs one month after ARV initiation. At enrollment, WLHIV had higher Shannon diversity and were more likely to have CST IV-B than CST I or III. After ARV initiation, α-diversity decreased in WLHIV but increased in HIV-negative women. Women initiating PrEP had a lower risk of sPTB compared to WLHIV initiating ART, but transitioning to CST IV during pregnancy increased the odds of sPTB. Larger studies are needed to explore ARV impact on pregnancy outcomes.},
}

Humans
Female
Pregnancy
Malawi
*HIV Infections/prevention & control/drug therapy/microbiology
*Vagina/microbiology
Adult
*Microbiota/drug effects
*Pregnancy Complications, Infectious/drug therapy/prevention & control/microbiology
Pre-Exposure Prophylaxis
Young Adult
*Anti-HIV Agents/therapeutic use
Premature Birth
*Bacteria/classification/genetics/isolation & purification/drug effects
*Anti-Retroviral Agents/therapeutic use
Pregnant People

@article {pmid40287196,
year = {2025},
author = {Altmäe, S and Rodríguez-Santisteban, A},
title = {Emerging targets for advancing endometrial therapeutics.},
journal = {Reproductive biomedicine online},
volume = {50},
number = {4},
pages = {104785},
doi = {10.1016/j.rbmo.2024.104785},
pmid = {40287196},
issn = {1472-6491},
mesh = {Humans ; Female ; *Endometrium/physiology/metabolism ; *Uterine Diseases/therapy ; Transcriptome ; },
abstract = {The endometrium plays a crucial role in female health. Globally, millions of women are affected by endometrial/uterine disorders, yet the endometrium and its role in gynaecological pathologies have been understudied. Gaining insight into the detailed endometrial architecture, gene expression, spatial and temporal cellular interactions, and microenvironment is essential for understanding the physiology and pathophysiology of this dynamic tissue. The current paper highlights the latest targets for advancing endometrial research that include single-cell RNA sequencing, spatial transcriptomics, the microbiome, organoid models, analysis of menstrual blood and the less-studied endometrial ageing. The authors hope that this summary will provide more insight into the novel methods, highlight advancing endometrial therapeutics and inspire readers to generate fresh ideas for future research avenues.},
}

Humans
Female
*Endometrium/physiology/metabolism
*Uterine Diseases/therapy
Transcriptome

@article {pmid40287170,
year = {2025},
author = {Bracamonte-Baran, W and Kim, ST},
title = {The Current and Future of Biomarkers of Immune Related Adverse Events.},
journal = {Immunology and allergy clinics of North America},
volume = {45},
number = {2},
pages = {223-249},
doi = {10.1016/j.iac.2025.01.010},
pmid = {40287170},
issn = {1557-8607},
abstract = {With their groundbreaking clinical responses, immune checkpoint inhibitors (ICIs) have ushered in a new chapter in cancer therapeutics. However, they are often associated with life-threatening or organ-threatening autoimmune/autoinflammatory phenomena, collectively termed immune-related adverse events (irAEs). In this review, we will first describe the mechanisms of action of ICIs as well as irAEs. Next, we will review biomarkers for predicting the development of irAEs or stratifying risks.},
}

@article {pmid40287068,
year = {2025},
author = {Häsler, R and Mikš, MH and Bajic, D and Soyyilmaz, B and Bendik, I and van Buul, VJ and Steinert, RE and Rehman, A},
title = {Human milk oligosaccharides modulating inflammation in infants, adults and older individuals - from concepts to applications.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100433},
doi = {10.1016/j.advnut.2025.100433},
pmid = {40287068},
issn = {2156-5376},
abstract = {The increasing global prevalence of inflammatory diseases such as ulcerative colitis and irritable bowel syndrome, represents a challenging task for healthcare systems. Several approaches to disease management target the intestinal microbiome, which plays a key role in health and disease. One promising approach is modulating the microbiome using human milk oligosaccharides (HMOs). Originating from human milk, HMOs are indigestible carbohydrates which act in a host-optimized prebiotic fashion by providing an energy source for health-promoting intestinal bacteria and exhibiting systemic effects. Commercial products supporting infant health and development have been the primary fields of HMO application. Advancements in the large-scale production of HMOs through bioengineering and precision fermentation have led to evaluating their potential for managing inflammatory diseases. Several in vitro studies and observations on model systems have been clinically validated in infants, resulting in a large body of evidence supporting the safety and efficacy of HMOs in inflammatory disorders. While novel approaches seek to explore interventions in adults, the primary goal for the future is to provide cost-efficient, safe, and reliable healthcare compounds across all age groups.},
}

@article {pmid40286937,
year = {2025},
author = {Zhang, X and Li, Y and Pei, Y and Yu, C and Zhang, X and Cao, F},
title = {Association between maternal stress patterns and neonatal meconium microbiota: A prospective cohort study.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2025.04.120},
pmid = {40286937},
issn = {1573-2517},
abstract = {BACKGROUND: This study aimed to identify maternal stress patterns and investigate their associations with neonatal meconium microbiota.

METHODS: A total of 465 pregnant women reported their stress conditions, including depression, anxiety, pregnancy-related anxiety, perceived stress, sleep, fear of birth, life events, and adverse childhood experiences. Meconium samples were collected from 348 newborns. Latent class analysis was used to identify the patterns of maternal stress.

RESULTS: Three group profiles were identified: "high negative emotion," "high ACEs-low negative emotion," and "low stress." the high ACEs-low negative emotion group and low stress group had higher levels of Chao1 diversity than the high negative emotion group (B = 0.25, P < 0.001; B = 0.18, P < 0.001, respectively). The high ACEs-low negative emotion group had higher levels of Chao1 diversity than the low stress group (B = 0.08, P = 0.001). The variations were observed in the abundance of Bacteroidetes, unidentified_Muribaculaceae, unclassified_Lachnospiraceae, unclassified_Clostridiales, unidentified_Bacteroidales, Oscillospira, and Ruminococcus among different maternal stress patterns.

LIMITATIONS: We did not analyze maternal microbiome samples and assessed the gut microbiota at only one time point.

CONCLUSIONS: These findings emphasized the need for a comprehensive approach to prenatal care that extends beyond traditional medical interventions. Addressing maternal stress through targeted support and interventions may help newborns benefit from a more favorable gut microbiota landscape.},
}

@article {pmid40286617,
year = {2025},
author = {Kang, S and Lee, JY and Natsagdorj, A and Matsuki, A and Cho, KS},
title = {Functional adaptation of PM2.5 microbiomes to varying environmental conditions in Northeast Asia: Ulaanbaatar, Seoul, and Noto.},
journal = {The Science of the total environment},
volume = {979},
number = {},
pages = {179495},
doi = {10.1016/j.scitotenv.2025.179495},
pmid = {40286617},
issn = {1879-1026},
abstract = {This study examined the bacterial and fungal communities associated with PM2.5 collected from three geographically distinct locations in Northeast Asia-Ulaanbaatar (high pollution), Seoul (moderate pollution), and Noto (low pollution)-which collectively represent a gradient of urbanization and environmental conditions during the spring sampling period from March 15 to April 7, 2022. Ulaanbaatar exhibited the highest abundance of both bacteria and fungi, yet exhibited the lowest fungal diversity. In contrast, Noto exhibited the lowest microbial abundance but the highest fungal diversity, while Seoul displayed intermediate values. Dominant bacterial genera, including Caldalkalibacillus, Halomonas, and Nesterenkonia, demonstrated notable resilience across all three locations, highlighting their adaptability to diverse environmental conditions. The dominant fungal genera were Cladosporium and Candida. Analyses revealed significant correlations between microbial community structures and environmental factors. In Ulaanbaatar, microbial communities were strongly associated with meteorological parameters such as temperature, humidity, and wind speed. In Seoul, stronger correlations were observed with polycyclic aromatic hydrocarbons (PAHs). Noto exhibited weaker correlations with both meteorological factors and organic compounds. Across all sites, bacteria consistently showed broader niche breadths compared to fungi, reflecting their greater metabolic versatility and resource utilization capacity. Both bacterial and fungal niche breadths generally increased at intermediate concentrations of alkanes and DCAs but declined at extreme concentrations, suggesting optimal survival ranges. These findings highlight the complex interplay of environmental factors and pollutants in shaping microbial community structures and functional diversity across diverse geographical settings during the spring season.},
}

@article {pmid40286573,
year = {2025},
author = {Pipová, M and Jevinová, P and Semjon, B and Regecová, I and Marcinčák, S and Nagy, J},
title = {Effect of feed supplementation with humic substances on phenotypic resistance profiles of Escherichia coli isolates from the ceca of broiler chickens.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105175},
doi = {10.1016/j.psj.2025.105175},
pmid = {40286573},
issn = {1525-3171},
abstract = {Humic substances (HS), natural complex-forming feed additives, are believed to reduce the bioavailability of antimicrobials to the gut microbiome, thereby limiting the emergence and spread of antimicrobial resistance in the food chain. However, this hypothesis has not yet been adequately verified experimentally. Our study was focused on the isolation of Escherichia coli (E. coli) from the ceca of 80 broiler chickens bred for 37 d under controlled conditions. Chickens in the control and experimental groups (40 broilers each) were fed standard commercial feeds, but the diet for experimental chicken was permanently supplemented with HS (99.3% feed + 0.7% HS). After slaughter and evisceration at the end of fattening period, the cecal contents of all chickens were subjected to microbiological analysis aimed at the enumeration, isolation and genotypic identification of E. coli strains by the species-specific PCR method. In total, 58 E. coli strains from control chickens and 60 strains from HS-fed chickens were tested for resistance against 19 antimicrobials using the broth microdilution method based on minimum inhibitory concentration breakpoints. Resistance to at least one antimicrobial was detected in almost 90% of E. coli isolates from control chickens, but in only 68.33% of isolates from HS-fed broilers (P < 0.01). In the experimental group, a noticeable decrease in resistance rates for ampicillin (31.78%), trimethoprim (22.88%), sulfamethoxazol (20.86%), and tetracycline (19.71%) was observed. The effect for fluorochinolones was less pronounced (0.09 ≤ P < 0.90). Feed supplementation with HS also reduced the prevalence of multidrug resistance (20.0% vs. 43.1%; P < 0.01) and led to a complete elimination of co-resistance to six and more antimicrobial classes. Additionally, no extended-spectrum beta-lactamase production could be predicted for E. coli isolates from HS-fed broilers. This is probably the first experimental study demonstrating a direct beneficial effect of HS-supplemented diet on the phenotypic resistance profiles of E. coli isolates from the ceca of commercially raised broiler chickens, showing that HS as feed additives can effectively reduce the phenotypic expression of antimicrobial resistance in E. coli.},
}

@article {pmid40286292,
year = {2025},
author = {Dai, Y and Wu, D and Carroll, I and Zou, F and Zou, B},
title = {High-dimensional Biomarker Identification for Interpretable Disease Prediction via Machine Learning Models.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf266},
pmid = {40286292},
issn = {1367-4811},
abstract = {MOTIVATION: Omics features, often measured by high-throughput technologies, combined with clinical features, significantly impact the understanding of many complex human diseases. Integrating key omics biomarkers with clinical risk factors is essential for elucidating disease mechanisms, advancing early diagnosis, and enhancing precision medicine. However, the high dimensionality and intricate associations between disease outcomes and omics profiles present substantial analytical challenges.

RESULTS: We propose a High-dimensional Feature Importance Test (HiFIT) framework to address these challenges. Specifically, we develop an ensemble data-driven biomarker identification tool, Hybrid Feature Screening (HFS), to construct a candidate feature set for downstream machine learning models. The pre-screened candidate features from HFS are further refined using a computationally efficient permutation-based feature importance test employing machine learning methods to flexibly model the potential complex associations between disease outcomes and molecular biomarkers. Through extensive numerical simulation studies and practical applications to microbiome-associated weight changes following bariatric surgery, as well as the examination of gene-expression-associated kidney pan-cancer survival data, we demonstrate HiFIT's superior performance in both outcome prediction and feature importance identification.

An R package implementing the HiFIT algorithm is available on GitHub (https://github.com/BZou-lab/HiFIT).

SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.},
}

@article {pmid40286136,
year = {2025},
author = {Bolesławska, I and Bolesławska-Król, N and Jakubowski, K and Przysławski, J and Drzymała-Czyż, S},
title = {Lactoferrin-A Regulator of Iron Homeostasis and Its Implications in Cancer.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {7},
pages = {},
doi = {10.3390/molecules30071507},
pmid = {40286136},
issn = {1420-3049},
mesh = {Humans ; *Lactoferrin/metabolism/pharmacology ; *Neoplasms/metabolism/drug therapy/pathology ; *Iron/metabolism ; *Homeostasis ; Animals ; Reactive Oxygen Species/metabolism ; Oxidative Stress/drug effects ; },
abstract = {Cancer is a global health challenge, and its development is closely linked to iron metabolism. Cancer cells have an increased demand for this element, which promotes their proliferation, invasion, and metastasis. Excess iron catalyzes the formation of reactive oxygen species (ROS), which can both induce ferroptosis and initiate oncogenic signaling pathways. The deregulation of iron metabolism in cancer patients leads to anemia or toxic iron overload and also affects the gut microbiota. Lactoferrin (LF), a glycoprotein with strong iron chelating properties, can regulate its availability to cancer cells, thereby limiting their growth and progression. By chelating free Fe ions, LF reduces oxidative stress and inhibits the mechanisms that promote carcinogenesis. Additionally, it exhibits immunomodulatory and anti-inflammatory effects and may enhance the body's anti-tumor response. This review analyses the mechanisms of action of lactoferrin in the context of cancer, with a particular focus on its chelating, antioxidant, and immunomodulatory properties. The multidirectional effects of LF make it a promising component of preventive and therapeutic strategies, requiring further clinical studies.},
}

Humans
*Lactoferrin/metabolism/pharmacology
*Neoplasms/metabolism/drug therapy/pathology
*Iron/metabolism
*Homeostasis
Animals
Reactive Oxygen Species/metabolism
Oxidative Stress/drug effects

@article {pmid40285661,
year = {2025},
author = {Yue, B and Gao, R and Zhao, L and Liu, D and Lv, C and Wang, Z and Ai, F and Zhang, B and Yu, Z and Geng, X and Wang, H and Wang, K and Chen, K and Liu, C and Wang, Z and Dou, W},
title = {β-Glucuronidase-Expressing Lactobacillus reuteri Triggers Irinotecan Enterotoxicity Through Depleting the Regenerative Epithelial Stem/Progenitor Pool.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2411052},
doi = {10.1002/advs.202411052},
pmid = {40285661},
issn = {2198-3844},
support = {82274329//National Natural Science Foundation of China/ ; 82130115//National Natural Science Foundation of China/ ; 82304991//National Natural Science Foundation of China/ ; 23YF1442500//Shanghai Science and Technology Committee Sailing Program Foundation/ ; },
abstract = {Irinotecan (CPT11)-induced diarrhea affects 80-90% of cancer patients due to β-glucuronidase (GUS) converting 7-ethyl-10-hydroxycamptothecin glucuronide (SN38G) to 7-ethyl-10-hydroxycamptothecin (SN38). It remains unclear whether SN38 impacts the homeostasis between gut microbiota and mucosal stem cell niche. This study explores the crosstalk between gut microbiota and intestinal stem cells (ISCs) in intestinal mucositis triggered by CPT11 chemotherapy. CPT11-treated mice exhibited significant colon shortening, inflammatory infiltration, intestinal barrier dysfunction, and ISC impairment, which correlated with gut dysbiosis, enrichment of GUS-expressing bacteria, and intraluminal SN38 accumulation. In contrast, antidiarrheal (Xianglian pill) treatment alleviated SN38-induced enterotoxicity and reduced GUS-expressing bacterial populations. Microbiome profiling of clinical patients and mucositis mice revealed a strong correlation between CPT11/SN38 enterotoxicity and GUS-expressing bacteria, particularly Lactobacillus reuteri. PLS-PM modeling further linked L. reuteri to impaired epithelial regeneration, which is validated using a 3D intestinal organoid model. L. reuteri hindered ISC differentiation into secretory lineages within the organoids. Furthermore, L. reuteri colonization in mice exacerbated mucositis and disrupted epithelial differentiation, while its elimination ameliorated colitis symptoms and preserved crypt cell stemness. These findings suggest that selectively targeting GUS-expressing bacteria, particularly L. reuteri, to protect the regenerative epithelial stem/progenitor pool may serve as an effective strategy for mitigating CPT11-induced enterotoxicity.},
}

@article {pmid40285477,
year = {2025},
author = {Hansen, SH and Maseng, MG and Grännö, O and Vestergaard, MV and Bang, C and Olsen, BC and Lund, C and Olbjørn, C and Løvlund, EE and Vikskjold, FB and Huppertz-Hauss, G and Perminow, G and Yassin, H and Valeur, J and Aass Holten, KI and Henriksen, M and Bengtson, MB and Ricanek, P and Opheim, R and Boyar, R and Torp, R and Frigstad, SO and Aabrekk, TB and Detlie, TE and Kristensen, VA and Strande, V and Hovde, Ø and Asak, Ø and Jess, T and Franke, A and Halfvarsson, J and Høivik, ML and Hov, JR},
title = {Fecal Microbiome Reflects Disease State and Prognosis in Inflammatory Bowel Disease in an Adult Population-Based Inception Cohort.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf060},
pmid = {40285477},
issn = {1536-4844},
support = {//Pfizer/ ; //Tillotts Pharma/ ; //Dam Foundation/ ; //Norwegian South-Eastern Health Authorities/ ; 2020066//Regional Health Authorities South-Eastern Norway/ ; 327634//Research Council of Norway/ ; //Bio-Me AS/ ; //DFG Excellence Cluster 2167/ ; //DFG Research Unit/ ; DNRF148//National Research Foundation/ ; },
abstract = {INTRODUCTION: We aimed to determine the diagnostic and prognostic potential of baseline microbiome profiling in inflammatory bowel disease (IBD).

METHODS: Participants with ulcerative colitis (UC), Crohn's disease (CD), suspected IBD, and non-IBD symptomatic controls were included in the prospective population-based cohort Inflammatory Bowel Disease in South-Eastern Norway III (third iteration) based on suspicion of IBD. The participants donated fecal samples that were analyzed with 16S rRNA sequencing. Disease course severity was evaluated at the 1-year follow-up. A stringent statistical consensus approach for differential abundance analysis with 3 different tools was applied, together with machine learning modeling.

RESULTS: A total of 1404 individuals were included, where n = 1229 samples from adults were used in the main analyses (n = 658 UC, n = 324 CD, n = 36 IBD-U, n = 67 suspected IBD, and n = 144 non-IBD symptomatic controls). Microbiome profiles were compared with biochemical markers in machine learning models to differentiate IBD from non-IBD symptomatic controls (area under the receiver operating curve [AUC] 0.75-0.79). For UC vs controls, integrating microbiome data with biochemical markers like fecal calprotectin mildly improved classification (AUC 0.83 to 0.86, P < .0001). Extensive differences in microbiome composition between UC and CD were identified, which could be quantified as an index of differentially abundant genera. This index was validated across published datasets from 3 continents. The UC-CD index discriminated between ileal and colonic CD (linear regression, P = .008) and between colonic CD and UC (P = .005), suggesting a location-dependent gradient. Microbiome profiles outperformed biochemical markers in predicting a severe disease course in UC (AUC 0.72 vs 0.65, P < .0001), even in those with a mild disease at baseline (AUC 0.66 vs 0.59, P < .0001).

CONCLUSIONS: Fecal microbiome profiling at baseline held limited potential to diagnose IBD from non-IBD compared with standard-of-care. However, microbiome shows promise for predicting future disease courses in UC.},
}

@article {pmid40284811,
year = {2025},
author = {Curadi, MC and Vallone, F and Tenuzzo, M and Gazzano, A and Gazzano, V and Macchioni, F and Vannini, C},
title = {Effect of Management System on Fecal Microbiota in Arabian Horses: Preliminary Results.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vetsci12040309},
pmid = {40284811},
issn = {2306-7381},
support = {PRA_2022_8//University of Pisa/ ; },
abstract = {The gut microbiota plays a basic role in maintaining the psychophysical health and well-being of horses. Understanding the complex interactions among microbial communities in relation to age, management, and health is a topic of growing interest. The equine microbiota, given its complexity, is subject to variations caused by internal or external stressors that can lead to metabolic problems and pathologies, i.e., obesity and laminitis. The aim of this study was to characterize the fecal microbiota of 12 purebred Arabian horses and to compare the microbial communities in two distinct management systems (Group 1 = box 22 h/day + paddock 2 h/day and Group 2 = paddock 24 h). Fecal samples were analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. The microbiota was predominantly composed of Firmicutes (32-53%) and Bacteroidetes (32-47.8%), with Ruminococcaceae emerging as the most prevalent bacterial family (10.9-24%). Comparisons of alpha and beta diversity revealed no statistically significant differences between the groups based on different management systems. This preliminary characterization contributes valuable data for understanding the equine fecal microbiota and lays the groundwork for future studies on the relationship among intestinal microbiota and equine health, performance, and management strategies.},
}

@article {pmid40284799,
year = {2025},
author = {Wang, Y and Cui, Q and Hou, Y and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Wang, W},
title = {Metagenomic Insights into the Diverse Antibiotic Resistome of Non-Migratory Corvidae Species on the Qinghai-Tibetan Plateau.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vetsci12040297},
pmid = {40284799},
issn = {2306-7381},
support = {2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; },
abstract = {Antibiotic resistance represents a global health crisis with far-reaching implications, impacting multiple domains concurrently, including human health, animal health, and the natural environment. Wild birds were identified as carriers and disseminators of antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). A majority of studies in this area have concentrated on migratory birds as carriers for the spread of antibiotic resistance over long distances. However, there has been scant research on the resistome of non-migratory Corvidae species that heavily overlap with human activities, which limits our understanding of antibiotic resistance in these birds and hinders the development of effective management strategies. This study employed a metagenomics approach to examine the characteristics of ARGs and mobile genetic elements (MGEs) in five common Corvidae species inhabiting the Qinghai-Tibetan Plateau. The ARGs were classified into 20 major types and 567 subtypes. Notably, ARGs associated with multidrug resistance, including to macrolide-lincosamide-streptogramins, tetracyclines, beta-lactam, and bacitracin, were particularly abundant, with the subtypes acrB, bacA, macB, class C beta-lactamase, and tetA being especially prevalent. A total of 5 types of MGEs (166 subtypes) were identified across five groups of crows, and transposase genes, which indicated the presence of transposons, were identified as the most abundant type of MGEs. Moreover, some common opportunistic pathogens were identified as potential hosts for these ARGs and MGEs. Procrustes analysis and co-occurrence network analysis showed that the composition of the gut microbiota shaped the ARGs and MGEs, indicating a substantial association between these factors. The primary resistance mechanisms of ARGs in crows were identified as multidrug efflux pumps, alteration of antibiotic targets, and enzymatic inactivation. High-risk ARGs which were found to potentially pose significant risks to public health were also analyzed and resulted in the identification of 81 Rank I and 47 Rank II ARGs. Overall, our study offers a comprehensive characterization of the resistome in wild Corvidae species, enhancing our understanding of the potential public health risks associated with these birds.},
}

@article {pmid40284786,
year = {2025},
author = {Samira, R and Monsur, M and Trina, NA},
title = {How the Built Environment Shapes Children's Microbiome: A Systematic Review.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040950},
pmid = {40284786},
issn = {2076-2607},
abstract = {This systematic review aims to synthesize key empirical findings to understand how various elements of the built environment influence the microbiome concerning children's health and well-being. A comprehensive literature search was conducted across multiple databases, focusing on studies that examined the relationship between built environment factors and the microbiome aspects of childhood. A total of 42 studies were included in the final systematic review. We analyzed these studies from a range of different lenses, starting with basic research questions and variables to types of built environments, age groups of children, sampling strategy, bioinformatics, and the biological methods utilized. This review highlights a growing emphasis on children's exposure to nature within built environments and its potential to beneficially alter the microbiome, with 38% of studies addressing this link. It also identifies a significant research gap in connecting built environment design features (landscape and/or architectural) to microbiome outcomes and associated health, behavioral, and mental health impacts on children. The findings indicate that interventions aimed at improving the built environment quality via design could foster healthier microbiomes in children's environments. This review underscores the need for interdisciplinary research and policy initiatives that integrate microbiome science with built environment design to promote children's health and well-being.},
}

@article {pmid40284784,
year = {2025},
author = {John, HT and Thomas, TC and Chukwuebuka, EC and Ali, AB and Anass, R and Tefera, YY and Babu, B and Negrut, N and Ferician, A and Marian, P},
title = {The Microbiota-Human Health Axis.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040948},
pmid = {40284784},
issn = {2076-2607},
support = {//UNIVERSITY OF ORADEA/ ; },
abstract = {Trillions of microorganisms play a pivotal role in maintaining health and preventing disease in humans. Their presence influences daily life, habits, energy levels, and pathologies. The present narrative review synthesized recent studies of microbial diversity across organ systems. The composition of the microbiota regulates the intestinal barrier, modulates the immune response, influences metabolism, and produces essential compounds such as short-chain fatty acids and neurotransmitters. Dysbiosis is associated with numerous pathologies, including metabolic, autoimmune, neurodegenerative, and cardiovascular diseases. The microbiota is key to maintaining physiological balance and reducing disease risk. Therapeutic interventions, such as probiotics, prebiotics, postbiotics, and microbiome transplantation, offer promising perspectives in restoring microbial homeostasis and preventing chronic diseases.},
}

@article {pmid40284783,
year = {2025},
author = {Ma, J and Peng, Q and Chen, S and Liu, Z and Zhang, W and Zhang, C and Du, X and Sun, S and Peng, W and Lei, Z and Zhang, L and Su, P and Zhang, D and Liu, Y},
title = {Microbiome Migration from Soil to Leaves in Maize and Rice.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040947},
pmid = {40284783},
issn = {2076-2607},
support = {2024CX36//Agricultural Science and Technology Innovation Program of Hunan Province/ ; 2024CX67//Agricultural Science and Technology Innovation Program of Hunan Province/ ; },
abstract = {The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant-microbe interactions for sustainable agriculture.},
}

@article {pmid40284777,
year = {2025},
author = {Liu, H and Chen, A and Wang, W and Peng, W and Mao, K and Yang, Y and Wu, Q and Zeng, M and Wang, K and Han, J and Zhou, H},
title = {Analysis of Fecal Microbiome and Metabolome Changes in Goats When Consuming a Lower-Protein Diet with Varying Energy Levels.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040941},
pmid = {40284777},
issn = {2076-2607},
support = {NO. 324QN301//Hainan Provincial Natural Science Foundation of China/ ; No:1630012025809//Central Public-interest Scientific Institution Basal Research Fund/ ; },
abstract = {The objective of this study was to evaluate the effect of fecal bacterial community and metabolomics in goats when consuming a lower-protein diet with different energy levels. Eight healthy Leizhou goats, with 11 ± 0.78 kg of body weight, were selected and housed individually in cages. The animals were randomly allocated to a lower-protein diet that varied with four metabolites energy levels (7.01, 8.33, 9.66, and 10.98 MJ/kg DM) in a replicated 4 × 4 Latin square design. Notably, energy-dependent microbial restructuring was observed at both phylum and genus levels. At the phylum level, the relative abundances of Firmicutes and Spirochaetote increased linearly, whereas the Bacteroidota and Patescibacteria decreased linearly with increasing dietary energy levels (p < 0.05). The relative abundances of Verrucomicrobiota increased quadratically, whereas others decreased quadratically with increasing dietary energy levels (p < 0.05). At the genus level, a total of 316 bacteria were identified in the 32 fecal samples. The relative abundances of Christensenellaceae_R-7_group, unclassified_f__Lachnospiraceae, Ruminococcus, norank_o__Clostridia_UCG-014, Treponema, [Eubacterium]_siraeum_group, and [Eubacterium]_ruminantium_group increased linearly, whereas the Oscillospiraceae_UCG-005, norank_f__[Eubacterium]_coprostanoligenes_group, Prevotellaceae_UCG-004, unclassified_c__Clostridia, norank_f__Ruminococcaceae, unclassified_f__ Oscillospiraceae, and others decreased linearly with an increasing dietary energy levels (p < 0.05). In addition, the metabolomic analysis of feces showed that there are many differential metabolites in goats when consuming a lower-protein diet with different energy levels; for example, lipid metabolism and amino acid metabolic pathways were increased in MLE, MHE, and HE groups compared to the LE group. In conclusion, this study provides further information regarding the effects on fecal bacterial community composition and metabolites in goats when consuming a lower-protein diet with different energy levels.},
}

@article {pmid40284772,
year = {2025},
author = {Madariaga-Troncoso, D and Vargas, I and Rojas-Villalta, D and Abanto, M and Núñez-Montero, K},
title = {Metataxonomics Characterization of Soil Microbiome Extraction Method Using Different Dispersant Solutions.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040936},
pmid = {40284772},
issn = {2076-2607},
support = {Fondecyt Iniciación 11230475//Agencia Nacional de Investigación y Desarrollo de Chile/ ; ANID Anillo ATE230007//Agencia Nacional de Investigación y Desarrollo de Chile/ ; },
abstract = {Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed soils; however, direct soil transfer presents practical limitations for large-scale applications. An alternative strategy involves extracting microbial communities through soil washing processes, but its success highly depends on proper microbiota characterization and efficient extraction methods. This study evaluated a soil wash method using four different dispersant solutions (Tween-80, NaCl, sodium citrate, and sodium pyrophosphate) for their ability to extract the majority of microbial cells from Antarctic and Crop soils. The extracted microbiomes were analyzed using 16S rRNA gene metataxonomics to assess their diversity and abundance. We found that some treatments extracted a greater proportion of specific taxa, and, on the other hand, some extracted a lower proportion than the control treatment. In addition, these dispersant solutions showed the extraction of the relevant microbial community profile in soil samples, composed of multiple taxa, including beneficial bacteria for soil health. Our study aims to optimize DNA extraction methods for microbiome analyses and to explore the use of this technique in various biotechnological applications. The results provide insights into the effect of dispersant solutions on microbiome extractions. In this regard, sodium chloride could be optimal for Antarctic soils, while sodium citrate is suggested for the Crop soils.},
}

@article {pmid40284767,
year = {2025},
author = {Wang, J and Geng, Y and Guo, J and Peng, J and Xu, H and Zhao, B and Huang, S and Qin, M and Du, W and Tian, J},
title = {The Subgingival Microbial Composition in Health and Periodontitis with Different Probing Depths.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040930},
pmid = {40284767},
issn = {2076-2607},
support = {82301078//National Natural Science Foundation of China/ ; PKUSS20220101//Research Foundation of Peking University School and Hospital of Stomatology/ ; },
abstract = {The differences in microbiota between periodontitis and health have been extensively studied; however, knowledge about how the microbiota shifts from shallow to deep periodontal pockets remains limited despite its clinical importance in disease progres-sion and management. Patients diagnosed with stage III periodontitis commonly pre-sent varied probing depths (PD) within the same oral cavity, reflecting localized disease severity. This study aims to analyze the microbiome of subgingival plaques at various PDs in periodontitis patients. Subgingival plaques were collected from sixteen healthy subjects (health group) and periodontal pockets of sixteen stage III periodontitis pa-tients (PD 0-3 mm, PD 4-5 mm and PD 6-9 mm groups). A total of 64 subgingival plaque samples underwent 16S rRNA gene sequencing. The PD 6-9 mm group exhib-ited significantly higher alpha diversity than the health group, and distinct subgingival microbial community structures were observed in periodontitis patients, regardless of probing depth. The relative abundance of specific genera differed notably between health and periodontitis states; Corynebacterium and Cardiobacterium decreased, whereas Schaalia increased in shallow pockets (PD 0-3 mm) of periodontitis relative to the health group. Co-occurrence network analysis on the species level revealed that the PD 4-5 mm group had the most complex interspecies interactions, followed by the PD 6-9 mm and PD 0-3 mm groups. These findings indicate significant variations in mi-crobial diversity, composition, and interspecies interactions associated with periodon-tal health and periodontitis severity, highlighting their potential relevance for clinical diagnosis and targeted therapeutic strategies.},
}

@article {pmid40284759,
year = {2025},
author = {Patel, NN and Gaiero, JR and Sulman, M and Moote, P and Nesbitt, D and Svircev, AM and Ellouze, W},
title = {Impact of Pre-Extraction Methods on Apple Blossom Microbiome Analysis.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040923},
pmid = {40284759},
issn = {2076-2607},
support = {J-002617; J-002861//Agriculture and Agri-Food Canada/ ; },
abstract = {This study examines the effect of pre-extraction methods, namely, sonication, grinding, and lyophilization, and the use of peptide nucleic acid (PNA) blockers on the DNA recovery, diversity, and taxonomic resolution of bacterial and fungal communities in apple blossoms. Sonication was the most successful in recovering bacterial 16S and fungal ITS reads across all the collection points and plots. Lyophilization and grinding led to a significant reduction in fungal read counts, while PNA enhanced the recovery of bacterial 16S reads. Sonication improved the efficiency of DNA extraction and yielded greater diversity in the recovered microbial community. Sonicated samples showed greater sensitivity to temporal shifts in microbial community composition. Communities in sonicated samples contained a larger number of bacterial genera, such as Bacillus, Staphylococcus, and Erwinia, and fungal genera, including Didymellaceae and Cladosporium. In contrast, lyophilization and grinding led to a reduction in detected taxa. The indicator species analysis determined that 35 bacterial and 21 fungal genera were closely related to sonication, whereas no other pre-extraction method had any associated genera. Our findings suggest that sonication is the most appropriate pre-extraction method for analyzing blossom-associated microbiomes, and that the use of PNA blockers can improve the recovery of bacteria and minimize contamination by host DNA.},
}

@article {pmid40284751,
year = {2025},
author = {Wang, XM and Huang, HJ and Sun, XW and Wei, RQ and Chen, HY and Liu, C and Liu, SJ},
title = {Identification and Characterization of Two Novel Members of the Family Eubacteriaceae, Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov., Isolated from Human Feces.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040916},
pmid = {40284751},
issn = {2076-2607},
support = {No. 82030116//National Natural Science Foundation of China/ ; tsqn202306036//Taishan Young/ ; },
abstract = {Members of Eubacteriaceae are involved in host health and diseases. Two Gram-stain-positive, strictly anaerobic, non-motile, non-spore-forming, and rod-shaped bacterial strains, HA2171[T] and HA2172[T], were isolated from the feces of Chinese healthy donors. Based on 16S rRNA gene sequences, HA2171[T] and HA2172[T] belonged to the family Eubacteriaceae. Physiological and biochemical characterizations indicated that HA2171[T] and HA2172[T] were neutrophilic, mesophilic, and tolerant to low-concentration NaCl. The major cellular fatty acids (>10.0%) of HA2171[T] were C16:0, C14:0, C18:1ω7c, and C17:0 2-OH, and those of HA2172[T] were C14:0 and C16:0. MK-6 was the respiratory quinone in both strains. Phylogenetic and phylogenomic analyses showed that HA2171[T] was closest to Anaerofustis stercorihominis ATCC BAA-858[T] and that HA2172[T] as closest to Pseudoramibacter alactolyticus ATCC 23263[T]. Genome annotation revealed that the HA2171[T] and HA2172[T] were able to metabolize carbohydrates and produce acetate and butyrate. HA2172[T] contains genes associated with hydrogen sulfide production, which is a potential risk for diseases. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, we propose that HA2171[T] and HA2172[T] represent two novel species, and the names Anaerofustis butyriciformans sp. nov. and Pseudoramibacter faecis sp. nov. are proposed.},
}

@article {pmid40284734,
year = {2025},
author = {Lobello, M and Bava, R and Castagna, F and Sotgiu, FD and Berlinguer, F and Tilocca, B},
title = {The Role of Vulture (Accipitriformes) Cutaneous Microbiota in Infectious Disease Protection.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040898},
pmid = {40284734},
issn = {2076-2607},
abstract = {Vultures (Accipitriformes), as obligate scavengers, are regularly exposed to a diverse array of pathogens present in decomposing carcasses. Nevertheless, they exhibit a remarkable ability to resist infections, suggesting a crucial role of skin microbiota in host defense. The microbial communities residing on necrophagic birds' skin create a protective barrier through competitive interactions, antimicrobial compound production, and immunity priming. Additionally, vultures contribute to ecosystem balance by reducing the spread of infectious agents. However, they may also serve as vectors for antimicrobial resistance (AMR) due to their exposure to contaminated food sources. Understanding the dynamics of their microbiota can provide valuable insights into host-microbe interactions, wildlife conservation, and public health. This review examines the composition and functional significance of vulture cutaneous microbiota. Specifically, it explores the role of necrophagic birds' skin microbiota in pathogen exclusion, immune system modulation, and environmental adaptation, with the aim of suggesting further research routes, besides clarifying the ecological implications of such birds.},
}

@article {pmid40284724,
year = {2025},
author = {Brinkerhoff, RJ and Pandian, J and Leber, M and Hauser, ID and Gaff, HD},
title = {Impacts of Tick Parasitism on the Rodent Gut Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040888},
pmid = {40284724},
issn = {2076-2607},
support = {5R01AI136035/GF/NIH HHS/United States ; },
abstract = {Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in treated versus control BALB/c mice. Whereas there is variation in the fecal microbiome associated with each of the host species we tested, some of the same microbial taxa, notably members of the family Muribaculaceae, occurred at higher relative abundance in tick-parasitized hosts in both the field and laboratory studies, suggesting that there are consistent impacts of tick parasitism on the host gut microbiome. We recommend future studies to test the hypothesis that epithelial cell secretions, generated as part of the host's immune response to tick parasitism, could provide resources that allow particular microbial lineages in the mammalian gut to flourish.},
}

@article {pmid40284718,
year = {2025},
author = {Wu, X and Liao, H and Zhang, X and Ma, Z and Fu, Z},
title = {Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040882},
pmid = {40284718},
issn = {2076-2607},
support = {2022GXNSFBA035473//Natural Science Foundation of Guangxi Province China/ ; 2023A1515011859//Guangdong Natural Science Foundation of China/ ; 2021KJQD18//Guangxi Minzu University Research Fund/ ; },
abstract = {Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m[2]) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.},
}

@article {pmid40284708,
year = {2025},
author = {Li, F and Jiang, D and Wang, Q and Chang, O and Yin, J and Yu, M and Pan, H},
title = {Host-Microbiota-Parasite Interactions in Grass Carp: Insights from Ichthyophthirius multifiliis Infection.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040872},
pmid = {40284708},
issn = {2076-2607},
support = {No.2024B03J1265//Guangzhou Municipal Science and Technology Bureau/ ; No.2023YFD2400504//the National Key R&D Program of China/ ; CARS-45//the earmarked fund for China Agriculture Research System/ ; 2023TD49，2024CG02//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {The ciliate parasite Ichthyophthirius multifiliis poses significant threats to grass carp (Ctenopharyngodon idellus) aquaculture. However, the limited understanding of host microbiota shifts and immune responses hinders effective control strategies. This study integrated analyses of host pathological indices, immune response and skin/gill/gut microbiota shifts after I. multifiliis infection. A histopathological examination identified gill and fin tissues embedded with I. multifiliis, accompanied by epithelial necrosis, and inflammatory cell infiltration. Biochemical profiling revealed marked elevations in aspartate aminotransferase (AST), alanine aminotransferase (ALT), urea (UREA), and creatinine (CREA) levels, indicating impaired hepatic and renal function. Quantitative RT-PCR analyses demonstrated the up-regulation of mucosal immune gene IgT and pro-inflammatory cytokine TNF-α while increasing the trend of systemic immune gene IgM. 16S rRNA sequencing revealed significant reductions in skin microbiota diversity. At the genus level, opportunistic pathogens Aeromonas and Vibrio proliferated in the intestine, whereas Flavobacterium and Candidatus Megaira increased in the skin and gills. Correlation analyses identified positive associations between Aeromonas/Vibrio abundance and host phenotype, contrasting with negative correlations observed for Sphingomonas, Acinetobacter, and Leifsonia. These findings demonstrate that I. multifiliis infection induces host microbiome dysbiosis and potentially opportunistic bacterial infections. This investigation advances our understanding of tripartite host-microbiota-parasite interactions and supports microbial community-based parasitosis control in fish culture.},
}

@article {pmid40284707,
year = {2025},
author = {Mennitti, C and Calvanese, M and Gentile, A and Vastola, A and Romano, P and Ingenito, L and Gentile, L and Veneruso, I and Scarano, C and La Monica, I and Di Lorenzo, R and Frisso, G and D'Argenio, V and Lombardo, B and Scudiero, O and Pero, R and Laneri, S},
title = {Skin Microbiome Overview: How Physical Activity Influences Bacteria.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040868},
pmid = {40284707},
issn = {2076-2607},
abstract = {The skin cannot be considered as just a barrier that protects against physical, chemical, and biological damage; it is a complex and dynamic ecosystem that varies across lifespans. Interest in the relationship between physical activity and skin microbiota has grown significantly in recent years. The skin microbiota has a crucial role in skin functions and physiology, and an imbalance, known as dysbiosis, is correlated with several diseases, such as inflammatory bowel disease (IBD), infectious disease, obesity, allergic disorders, and type 1 diabetes mellitus. Among the causes of dysbiosis, the practice of physical exercise, especially in contact sports, including wrestling, artistic gymnastics, and boating, certainly represents a predisposing factor for infectious disease. This review aims to provide an overview of the skin microbiota and its regulation, focusing on interactions between physical exercise and skin microbiota, the antimicrobial peptides (AMPs) as regulators of skin microbiota, and the impact of probiotics supplementation on physical performance.},
}

@article {pmid40284680,
year = {2025},
author = {Kumar, M and Yan, Y and Jiang, L and Sze, CH and Kodithuwakku, SP and Yeung, WSB and Lee, KF},
title = {Microbiome-Maternal Tract Interactions in Women with Recurrent Implantation Failure.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040844},
pmid = {40284680},
issn = {2076-2607},
support = {06173976//HMRF/ ; },
abstract = {Microorganisms play an important role in regulating various biological processes in our bodies. In women, abnormal changes in the reproductive tract microbiome are associated with various gynecological diseases and infertility. Recent studies suggest that patients with recurrent implantation failure (RIF) have a reduced genus Lactobacillus population, a predominant bacterial species in the vagina and uterus that protects the reproductive tract from pathogenic bacterial growth via the production of various metabolites (e.g., lactic acid, bacteriocin, and H2O2). Moreover, a higher percentage of pathogenic bacteria genera, including Atopobium, Gardnerella, Prevotella, Pseudomonas, and Streptococcus, was found in the uterus of RIF patients. This review aimed to examine the role of pathogenic bacteria in RIF, determine the factors altering the endometrial microbiome, and assess the impact of the microbiome on embryo implantation in RIF. Several factors can influence microbial balance, including the impact of extrinsic elements such as semen and antibiotics, which can lead to dysbiosis in the female reproductive tract and affect implantation. Additionally, probiotics such as Lacticaseibacillus rhamnosus were reported to have clinical potential in RIF patients. Future studies are needed to develop targeted probiotic therapies to restore microbial balance and enhance fertility outcomes. Research should also focus on understanding the mechanisms by which microorganisms generate metabolites to suppress pathogenic bacteria for embryo implantation. Identifying these interactions may contribute to innovative microbiome-based interventions for reproductive health.},
}

@article {pmid40284678,
year = {2025},
author = {Hu, H and Geng, S and Zhu, Y and He, X and Pan, X and Yang, M},
title = {Seed-Borne Endophytes and Their Host Effects.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040842},
pmid = {40284678},
issn = {2076-2607},
support = {32360255, 32471746 and 31560538;//National Natural Science Foundation of China/ ; },
abstract = {In the process of long-term co-evolution, endophytes and host plants benefit from and interact with each other, resulting in positive effects such as promoting plant growth, enhancing resistance, producing beneficial secondary metabolites, and negative effects such as carrying pathogens and producing toxins. In addition to the vegetative organs, plant seeds are also colonized by diverse endophytes and serve as vectors for the transmission of endophytes across plant generations. Seed endophytes, termed seed-borne endophytes (SBEs), have attracted much attention because these endophytes are involved in the assembly of the plant association microbiome and exert effects on progeny plants through vertical transfer. However, the importance of SBEs may still be underestimated. The present paper reviews the diversity, origin, and vertical transmission of seed endophytes, as well as their interaction and function with hosts, so as to provide a reference for future research and application of seed endophytes.},
}

@article {pmid40284650,
year = {2025},
author = {Adil, NA and Omo-Erigbe, C and Yadav, H and Jain, S},
title = {The Oral-Gut Microbiome-Brain Axis in Cognition.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040814},
pmid = {40284650},
issn = {2076-2607},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline and neuronal loss, affecting millions worldwide. Emerging evidence highlights the oral microbiome-a complex ecosystem of bacteria, fungi, viruses, and protozoa as a significant factor in cognitive health. Dysbiosis of the oral microbiome contributes to systemic inflammation, disrupts the blood-brain barrier, and promotes neuroinflammation, processes increasingly implicated in the pathogenesis of AD. This review examines the mechanisms linking oral microbiome dysbiosis to cognitive decline through the oral-brain and oral-gut-brain axis. These interconnected pathways enable bidirectional communication between the oral cavity, gut, and brain via neural, immune, and endocrine signaling. Oral pathogens, such as Porphyromonas gingivalis, along with virulence factors, including lipopolysaccharides (LPS) and gingipains, contribute to neuroinflammation, while metabolic byproducts, such as short-chain fatty acids (SCFAs) and peptidoglycans, further exacerbate systemic immune activation. Additionally, this review explores the influence of external factors, including diet, pH balance, medication use, smoking, alcohol consumption, and oral hygiene, on oral microbial diversity and stability, highlighting their role in shaping cognitive outcomes. The dynamic interplay between the oral and gut microbiomes reinforces the importance of microbial homeostasis in preserving systemic and neurological health. The interventions, including probiotics, prebiotics, and dietary modifications, offer promising strategies to support cognitive function and reduce the risk of neurodegenerative diseases, such as AD, by maintaining a diverse microbiome. Future longitudinal research is needed to identify the long-term impact of oral microbiome dysbiosis on cognition.},
}

@article {pmid40284643,
year = {2025},
author = {Thwe, MN and Moné, Y and Sen, B and Czerski, S and Azad, A and Earl, JP and Hall, DC and Ehrlich, GD},
title = {Microspatial Heterogeneities and the Absence of Postmortem Contamination in Alzheimer's Disease Brain Microbiota: An Alzheimer's Pathobiome Initiative (AlzPI) Study.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040807},
pmid = {40284643},
issn = {2076-2607},
support = {001//Dr. James Truchard/ ; 002//Bill and Marian Cook Foundation/ ; 003//Drexel University College of Medicine, Department of Microbiology and Immunology and the Institute for Molecular Medicine and Infectious Disease/ ; },
abstract = {The discovery of profound differences in the brain microbiota of Alzheimer's disease (AD) patients and age-matched controls (AMCs) raised questions of postmortem contamination and bacterial transport processes which could be informed by microspatial heterogeneities. We performed semiquantitative species-specific bacterial analyses on multiple micro biopsies from each of the 30 brain specimens (AD and controls). We trimmed ~1 mm of each specimen's edges for surface contaminants and made multiple sterile biopsy punches of the resultant core of each specimen. To identify species-specific abundances, we used our validated, semiquantitative, full-length 16S rRNA gene pan-domain amplification protocol followed by high-fidelity circular consensus sequencing performed on a Pacific Biosciences Sequel IIe instrument. Statistical analyses showed no significant increase in bacterial abundance on trimmed surfaces compared to core specimens, including C. acnes, the most abundant species previously identified in AD. We did find evidence of substantial bacterial species abundance differences among micro-biopsies obtained from within individual tissue blocks supporting our hypothesis of microspatial heterogeneities. The autopsy brain specimens used in our analyses in this study and our previous publication were not contaminated prior to or postharvesting but we suggest that future microbiological analyses of brain specimens include similar types of edge-core comparison analyses. Further, the species-level bacterial abundance heterogeneities among specimens of the same tissue suggest that multiple symbiotic processes may be occurring.},
}

@article {pmid40284630,
year = {2025},
author = {Zhang, Y and Wang, L and Peng, L},
title = {The Role of Intestinal Fungi in the Pathogenesis and Treatment of Ulcerative Colitis.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040794},
pmid = {40284630},
issn = {2076-2607},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease closely associated with dysbiosis of the gut microbiome, encompassing not only bacterial communities but also fungal populations. Despite the growing recognition of the gut microbiome's role in UC pathogenesis, the contribution of intestinal fungi has only recently garnered significant attention. In this review, we comprehensively examine the characteristics of intestinal fungi in both healthy individuals and UC patients, elucidating their role in disease pathogenesis and their interactions with bacterial communities. Additionally, we explore the impact of intestinal fungi on disease severity and therapeutic responses in UC. Furthermore, we evaluate the therapeutic potential of antifungal agents, probiotics, and fecal microbiota transplantation (FMT) in UC management, emphasizing the critical role of fungi in these treatment modalities. Future research should prioritize elucidating the multifunctional roles of fungi in UC pathogenesis and their implications for treatment strategies. Moreover, the identification of fungal biomarkers associated with FMT efficacy could pave the way for precision medicine approaches in FMT, offering novel insights into personalized therapeutic interventions for UC.},
}

@article {pmid40284628,
year = {2025},
author = {D'Accolti, M and Soffritti, I and Mazziga, E and Bini, F and Bisi, M and Volta, A and Mazzacane, S and Caselli, E},
title = {A Sustainable Combined Approach to Control the Microbial Bioburden in the School Environment.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040791},
pmid = {40284628},
issn = {2076-2607},
abstract = {The indoor microbiome is a dynamic ecosystem including pathogens that can impact human health. In this regard, the school environment represents the main living space of humans for many years, and an unhealthy environment can significantly condition students' health. School rooms can suffer from insufficient ventilation and the use of building materials that may favor pathogen contamination, mostly sanitized by conventional chemical-based methods, which can impact pollution, have temporary effects, and induce the selection of antimicrobial resistance (AMR) in persistent microbes. In the search for sustainable and effective methods to improve the healthiness of the classroom environment, a pre-post case-control study was performed in an Italian high school. Over a year, different interventions were sequentially placed and evaluated for their impact on bioburden and air quality, including the introduction of plants, a mechanical ventilation system, and probiotic-based sanitation (PBS) in substitution for chemical sanitation. Through continuous microbial monitoring of the enrolled school rooms, via culture-dependent and -independent methods, a remarkable bioburden level was detected at baseline (around 12,000 and 20,000 CFU/m[2], before and after classes, respectively), composed mostly of Staphylococcus spp. and fungi. Some decrease in fungal contamination was observed following the introduction of plants. Still, the most significant decrease in pathogens and associated AMR was detected following the introduction of ventilation and PBS, which decreased pathogen level by >80% (p < 0.001) and AMR by up to 3 Log10 (p < 0.001) compared to controls. Collected data support the use of combined strategies to improve indoor microbial quality and confirm that PBS can effectively control bioburden and AMR spread not only in sanitary environments.},
}

@article {pmid40284627,
year = {2025},
author = {Gupta, M and Cilkiz, M and Ibrahim, MMA and Athrey, G},
title = {Gut Microbiome-Brain Crosstalk in the Early Life of Chicken Reveals the Circadian Regulation of Key Metabolic and Immune Signaling Processes.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040789},
pmid = {40284627},
issn = {2076-2607},
support = {2019-67015-29441//Partly funded by USDA NIFA award/ ; },
abstract = {Circadian rhythms are innate biological systems that control everyday behavior and physiology. Furthermore, bilateral interaction between the host's circadian rhythm and the gut microbes influences a variety of health ramifications, including metabolic diseases, obesity, and mental health including GALT physiology and the microbiome population. Therefore, we are studying the correlation between differential gene expression in the chicken brain and microbiota abundance during circadian rhythms. To understand this, we raised freshly hatched chicks under two photoperiod treatments: normal photoperiod (NP = 12/12 LD) and extended photoperiod (EP 23/1 LD). The chicks were randomly assigned to one of two treatments. After 21 days of circadian entrainment, the chicks were euthanized at nine time points spaced six hours apart over 48 h to characterize the brain transcriptomes. Each sample's RNA was extracted, and 36 mRNA libraries were generated and sequenced using Illumina technology, followed by data processing, count data generation, and differential gene expression analysis. We generated an average of 17.5 million reads per library for 237.9 M reads. When aligned to the Galgal6 reference genome, 11,867 genes had detectable expression levels, with a common dispersion value of 0.105. To identify the genes that follow 24 h rhythms, counts per million data were performed in DiscoRhythm. We discovered 577 genes with Cosinor and 417 with the JTK cycle algorithm that exhibit substantial rhythms. We used weighted gene co-expression network analysis (WGCNA) to analyze the correlation between differentially expressed genes and microbiota abundance. The most enriched pathways included aldosterone-regulated sodium reabsorption, endocrine and other factor-regulated calcium reabsorption, GABAergic synapse, oxidative phosphorylation, serotonergic synapse, dopaminergic synapse and circadian entrainment. This study builds on our previous study, and adds new findings about the specific interactions and co-regulation of the brain transcriptome and the gut microbiota. The interaction between gut microbiota and host gene expression highlights the potential benefits of microbiome-modulation approaches to improve gut health and performance in poultry.},
}

@article {pmid40284600,
year = {2025},
author = {Esiobu, N and Dawkins, K and Sanhaji, Y and Voorn, M and Murillo, K and Hill, Z and Naeem, F and Edouard, J and McCorquodale, D},
title = {Rhizosphere Microbiomes of Citrus Plants in Historically Undisturbed 100-Year-Old Groves Appear to Mitigate Susceptibility to Citrus Greening Disease.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040763},
pmid = {40284600},
issn = {2076-2607},
support = {2023-77040-41197//USDA NIFA/ ; },
abstract = {Microbiome studies aimed at combating the citrus greening devastation caused by Liberibacter asiaticus abound. However, the role of farming practices, such as the massive use of herbicides, pesticides, and inorganic fertilizers on specific taxa and plant population immunity remains an important inquiry. To test our hypothesis that agricultural practices in managed Citrus groves induce root microbiome dysbiosis, potentially rendering citrus readily susceptible to citrus greening disease (CGD), we compared the CGD and root microbiome status of citrus plants in a rare > 130-year-old grove (no anthropogenic influence) to those of managed Valencia groves (symptomatic and asymptomatic). Citrus greening disease was detected by qPCR using the HLBa/HLBs/HLBp primer/probe combination, while root microbiome community structure was determined using 16S rDNA amplicon sequencing. The prevalence of CGD among citrus growing in the undisturbed, healthy soils was zero (Ct values > 36), while symptomatic and asymptomatic Valencia from managed groves was 100% positive (Ct < 34). Known beneficial plant symbionts (Actinomycetales, Bradyrhizobium, Verrucomicrobia, etc.) from Phylum Actinobacteria and Proteobacteria were depleted in the rhizosphere of the managed sites. This dysbiotic shift was characterized by enrichment with Acidobacterium, Nitrospira, and Sphingomonas spp. In highly infected Valencia oranges, beneficial taxa of the Alphaproteobacteria declined significantly (from 20-25% to 10-15%), while Bacillus sp. (a Firmicutes) was enriched 13-fold. Simpson and Shannon diversity indices were similar for all plant microbiomes except the heavily infected Valencia, which exhibited low diversity (p < 0.05), indicating that diversity indices alone are not reliable measures of soil health or rhizobiome homeostasis. Large reservoirs of known and novel putative beneficial rhizosphere microbes in undisturbed sites supported zero CGD, despite proximity to the managed sites where diverse non-beneficial taxa coincided with high disease rates. Supplementing the use of agrochemicals with carefully designed microbial products for plant disease control and sustainable soil health deserves acute attention.},
}

@article {pmid40284595,
year = {2025},
author = {Frazier, AN and Willis, W and Robbe, H and Ortiz, A and Koziel, JA},
title = {Characterization and Assembly Dynamics of the Microbiome Associated with Swine Anaerobic Lagoon Manure Treated with Biochar.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040758},
pmid = {40284595},
issn = {2076-2607},
support = {3090-31630-006//USDA-ARS CRIS/ ; },
abstract = {Biochar has significant potential for livestock microbiomes and crop agriculture regarding greenhouse gas emissions reduction. Therefore, a pilot study was designed to investigate the effect of biochar application on the surface of swine manure from an open lagoon and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse biochar (n = 4), fine biochar (n = 4), and ultra-fine biochar (n = 4). Additionally, aged manure in bulk was collected (n = 4) to assess alterations from the control group. The method of 16S rRNA amplicon sequencing along with microbial analyses was performed. Diversity was significantly different between aged manure in bulk samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Differential abundance analysis revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. Stochastic and functional analyses revealed that biochar treatments were not deterministically altering assembly patterns, and functional redundancy was evident regardless of compositional shifts.},
}

@article {pmid40284586,
year = {2025},
author = {Khan, MZ and Li, Y and Zhu, M and Li, M and Wang, T and Zhang, Z and Liu, W and Ma, Q and Wang, C},
title = {Advances in Donkey Disease Surveillance and Microbiome Characterization in China.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040749},
pmid = {40284586},
issn = {2076-2607},
support = {2022YFD1600103; 2023YFD1302004//the National Key R&D Program of China/ ; SDAIT-27//the Shandong Province Modern Agricultural Technology System Donkey Industrial Innovation Team/ ; 19211162//Livestock and Poultry Breeding Industry Project of the Ministry of Agriculture and Rural Affairs/ ; SDNYXTTG-2024-13//the Shandong Province Agricultural Major Technology Collaborative Promotion Plan/ ; GDWZ202401//the Liaocheng Municipal Bureau of Science and Technology, High-talented Foreign Expert Introduction Program/ ; },
abstract = {This review article highlights the surveillance of bacterial, viral, and parasitic diseases in donkey populations in China. Key findings highlight significant threats from Equine herpesviruses (EHV-8 and EHV-1), which cause encephalitis, abortion, and respiratory distress. Several parasitic infections including Giardia duodenalis, Cryptosporidium spp., Enterocytozoon bieneusi, and Toxoplasma gondii present important zoonotic concerns across multiple regions of China. Additionally, this review synthesizes current knowledge on donkey microbiota across various body sites and examines their functional significance in health and disease. The complex relationship between the microbiota and host health represents a critical area of research in donkeys. Recent molecular advancements have enhanced our understanding of the diverse microbial ecosystems inhabiting different body sites in donkeys and their profound impact on health outcomes. As single-stomach herbivores, donkeys possess complex microbial communities throughout their digestive tracts that are essential for intestinal homeostasis and nutritional processing. Significant variations in microbiota composition exist across different intestinal segments, with the hindgut displaying greater richness and diversity compared to the foregut. Beyond the digestive system, distinct microbial profiles have been characterized across various body sites including the skin, oral cavity, reproductive tract, and body secretions such as milk. The health implications of donkey microbiota extend to critical areas including nutrition, immune function, and disease susceptibility. Research demonstrates how dietary interventions, environmental stressors, and physiological states significantly alter microbial communities, correlating with changes in inflammatory markers, antioxidant responses, and metabolic functions. Additionally, specific microbial signatures associated with conditions like endometritis and respiratory disease suggest the potential for microbiota-based diagnostics and therapeutics. The identification of antibiotic-resistant strains of Proteus mirabilis and Klebsiella pneumoniae in donkey meat highlights food safety concerns requiring enhanced monitoring systems and standardized safety protocols. These findings provide a foundation for improved donkey healthcare management, including targeted disease surveillance, microbiota-based interventions, and protective measures for those working with donkeys or consuming donkey-derived products.},
}

@article {pmid40284573,
year = {2025},
author = {Russell, G and Alegoz, R and Hester, K and Sierzega, KL and Szul, MJ and Hubert, N and Rylander, T and Jensen, S and Ciancio, MJ and Martinez-Guryn, K and Evans, CC},
title = {The Microbiome of an Outpatient Sports Medicine Clinic During a Global Pandemic: Effects of Implementation of a Microbiome-Specific Cleaning Program.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040737},
pmid = {40284573},
issn = {2076-2607},
support = {2018//Illinois Physical Therapy Association/ ; 2020//Illinois Physical Therapy Association/ ; },
abstract = {Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. Hand sanitizer containing a fluorescent probe used by patients and staff identified surface contact. High-contact surfaces were analyzed for bacterial DNA and SARS-CoV-2. A microbiome-specific cleaning and hygiene plan was developed based on initial analysis. After the implementation of the revised cleaning regimen, microbial community diversity and predicted metagenome content (PICRUSt) were employed for differential analysis. Patients had greater surface contact than staff. Ralstonia pickettii was the dominant species pre-cleaning, comprising 49.76% of the total, and observed on 79.5% of surfaces. The cleaning and hygiene plan significantly increased Shannon diversity, and R. pickettii decreased to 4.05% of total bacteria. SARS-CoV-2 was not observed on any surfaces. This study found ecological dominance by a single species in this outpatient clinic, suggesting a potential source of HAIs. However, a microbiome-specific cleaning strategy was successful in diversifying the microbiome and reducing ecological dominance. Additional research is needed to confirm these findings.},
}

@article {pmid40284569,
year = {2025},
author = {Skidmore, AM and Bradfute, SB},
title = {Bacterial DNA Contamination of Commercial PCR Enzymes: Considerations for Microbiome Protocols and Analysis.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040732},
pmid = {40284569},
issn = {2076-2607},
support = {1P20GM103451-01A1/NH/NIH HHS/United States ; 1K12GM088021-01A1/NH/NIH HHS/United States ; },
abstract = {The microbiome remains a top area of research, and it is now common to examine any organic and inorganic samples for bacterial colonization. However, due to the ubiquity of bacteria in the environment, separating the low-burden colonization of bacteria from the possible contamination of laboratory reagents remains problematic. When examining samples of expected low bacterial burden, it is common to first amplify any bacterial DNA present through PCR before sequencing. In this work, we examined nine different commercial PCR enzymes and their reaction components as possible sources of bacterial DNA contamination. We found contaminating bacterial DNA in seven of the nine reactions, and this DNA was shown to come from a variety of species. Importantly, we were able to perform these studies solely with endpoint PCR and Sanger sequencing, which are more accessible and affordable than high-throughput, short-read sequencing and real-time PCR. This work confirms that there needs to be an increased emphasis on including control reactions in microbiome studies so that contaminating DNA sequences can be identified and addressed, and that this can be achieved with minimal resources.},
}

@article {pmid40284562,
year = {2025},
author = {Stefanis, C and Tsigalou, C and Bezirtzoglou, I and Voidarou, CC and Stavropoulou, E},
title = {Microbiome Research in Greece: A Comprehensive Bibliometric Study.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040725},
pmid = {40284562},
issn = {2076-2607},
abstract = {Bibliometric analyses are increasingly used to evaluate scientific domains, revealing research trends, productivity, and impact. This study provides a bibliometric analysis of microbiome-related research conducted by Greek scientists. Data were retrieved from the Scopus database, using the keyword "microbiome" (English) for publications until December 2024. Bibliometric analysis was performed using VOSviewer and the bibliometrix package in R. Our findings indicate that research output has increased exponentially since 2018, with the National and Kapodistrian University of Athens and the Aristotle University of Thessaloniki leading microbiome research in Greece. Medicine, biochemistry, genetics, molecular biology, immunology, and microbiology are the predominant research fields. The keyword analysis highlights "microbiome", "microbiota", "probiotics", "prebiotics", "intestinal flora", and "16S rRNA" as central topics. Additionally, we acknowledge the role played by alternative microbial markers, including 18S rRNA/ITS sequencing, for fungal diversity studies. This bibliometric study demonstrates a dynamic and evolving research landscape in Greece and highlights the international relevance of Greek contributions to microbiome science.},
}

@article {pmid40284560,
year = {2025},
author = {Chen, X and Niu, Q and Li, J and Zhou, Z and Wu, Y and Song, G and Liu, R},
title = {Anaerobic Digestion of High-Solid Chicken Manure (CM) at Different Temperature: Intestinal Microbiome Efficiency, Inhibition, and Microbial Community Evolution.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040724},
pmid = {40284560},
issn = {2076-2607},
support = {51608304//National Natural Science Foundation of China/ ; ZR2024MB158//Shandong Provincial Natural Science Foundation/ ; 2022YFC3700187//National High Technology Research and Development Program of China/ ; },
abstract = {Anaerobic digestion (AD) of high-solid mono-chicken manure (CM) holds great promise for resource utilization. However, the effects of substrate overload (high-solid mixture inside the reactor) on AD performance at various temperatures are still unclear, moreover, the metabolic processes with and without inoculation are also seldom reported. In this study, three key impact factors of different temperatures (4 °C, 35 °C, 55 °C and 75 °C), total solids (TS) inside, and inoculation were conducted to comprehensively explore the process variation. EEM-FRI results revealed that high temps boost coenzyme F420, while TS predominately driver the microbial production. High TS and temperature synthetically result in high free ammonia (FA) (>600 mg/L) associated with free volatile fatty acid (FVFA) (>450 mg/L), reducing CH4 production but increasing VFAs accumulation (12 g/L at 55 °C). Notably, intestinal microbiota alone without inoculation even achieved 11 g/L of VFA. The cross-feeding symbiosis between fermentative bacteria (Caldicoprobacter, Bacteroidetes, Tepidimicrobium) and hydrogenotrophic Methanobacterium enhanced CH4 production (68 mL/gVS at 35 °C). Moreover, high temperatures reduced microbial diversity but made heat-resistant hydrolytic bacteria dominant. This study precisely analyzes the effects of temperature and inoculation factors on the acidification efficiency of high-solid CM digestion, providing a crucial scientific basis for optimizing the resource utilization of CM waste.},
}

@article {pmid40284547,
year = {2025},
author = {Alzahrani, AJ and Al-Hebshi, BM and Yahia, ZA and Al-Judaibi, EA and Alsaadi, KH and Al-Judaibi, AA},
title = {Impact of Microbiota Diversity on Inflammatory Bowel Disease.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040710},
pmid = {40284547},
issn = {2076-2607},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition that includes two main types, Crohn's disease (CD) and ulcerative colitis (UC), involving inflammation of the gastrointestinal (GI) tract. The exact cause of IBD is unknown but could be a combination of genetic, environmental, and immune system factors. This study investigated the impact of IBD on microbiota diversity by evaluating the differences in microbial composition and the microbiota of a control group (A) of healthy individuals and a group (B) of IBD patients. Sixty biopsies were collected from participants recruited from hospitals in Makkah, Saudi Arabia. Biopsy specimens were taken during colonoscopy examination, and bacterial identification was performed by extracting ribosomal DNA from sigmoid colon biopsies using a DNeasy Blood & Tissue Kit. Metagenomics and bioinformatics analyses were then conducted to analyze and compare the microbiota in the two groups. The results showed that the varieties of core microbiome species were 3.81% greater in the IBD patients than in the members of the control group. Furthermore, the differences between the groups were significantly greater than the variations within each group. Differences between the two groups were detected in the relative abundance of Clostridium nexile, Ruminococcus gnavus, Ruminococcus faecis, and Escherichia coli. These results indicate that microbiota could play a role in the pathogenesis of IBD and suggest that microbial diversity can serve as a biomarker for diagnosing the disease and monitoring its progression.},
}

@article {pmid40284482,
year = {2025},
author = {Ćorović, M and Petrov Ivanković, A and Milivojević, A and Pfeffer, K and Homey, B and Jansen, PAM and Zeeuwen, PLJM and van den Bogaard, EH and Bezbradica, D},
title = {Investigating the Effect of Enzymatically-Derived Blackcurrant Extract on Skin Staphylococci Using an In Vitro Human Stratum Corneum Model.},
journal = {Pharmaceutics},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics17040487},
pmid = {40284482},
issn = {1999-4923},
support = {451-03-136/2025-03/200135 and 451-03-136/2025-03/200287//Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; 7750109//Science Fund of the Republic of Serbia, programme IDEAS/ ; 101060130//Horizon Europe 2021-2027 research and innovation program/ ; },
abstract = {Background/Objectives: Numerous intrinsic and extrinsic stressors can disrupt the balance of the skin microbiome, leading to the development of various skin diseases. It has been proven that coagulase-negative staphylococci (CoNS) are important commensals for maintaining skin microbiome homeostasis and fighting cutaneous pathogens such as Staphylococcus aureus (S. aureus). Here, we examined the influence of polyphenol-rich enzymatic blackcurrant extract (EBCE) on pathogenic coagulase-positive S. aureus strains and beneficial CoNS, like Staphylococcus epidermidis (S. epidermidis), to explore its potential for rebalancing the skin microbiota. Methods: The polyphenol profile of EBCE was determined by ultra-high-pressure liquid chromatography-tandem mass spectrometry. Microwell plate assays were employed to study the effect of EBCE on five S. aureus strains isolated from the skin of atopic dermatitis patients. An in vitro human stratum corneum model was used to test its effect on mixed bacterial cultures. Results: EBCE inhibited the growth of all tested S. aureus strains by 80-100% at the highest tested concentration after 7 h. No microbial growth was observed at the highest tested EBCE concentration using the stratum corneum model inoculated with one selected pathogen (S. aureus SA-DUS-017) and one commensal laboratory strain (S. epidermidis DSM 20044). The lowest tested concentration did not interfere with S. aureus growth but strongly stimulated the growth of S. epidermidis (~300-fold colony forming unit increase). In addition, low EBCE concentrations strongly stimulated CoNS growth in microbiome samples taken from the armpits of healthy volunteers that were spiked with S. aureus SA-DUS-017. Conclusions: These preclinical data support further testing of EBCE-enriched topical preparations as potential cutaneous prebiotics in human studies.},
}

@article {pmid40284471,
year = {2025},
author = {Malinauskiene, V and Cijauskaite, E and Sadauskaite, G and Stundiene, I},
title = {Role of Gut Microbiota and Metabolomics in Predicting Response to Vedolizumab in Inflammatory Bowel Disease: A Systematic Review.},
journal = {Pharmaceutics},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics17040476},
pmid = {40284471},
issn = {1999-4923},
abstract = {Background: This review explores the impact of gut microbiota profiles in predicting the response to anti-integrin biologic therapy, particularly vedolizumab, in inflammatory bowel disease (IBD) patients. IBD, encompassing Crohn's disease and ulcerative colitis, is a chronic inflammatory condition with a growing prevalence linked to industrialization and lifestyle changes. Disruption in the gut microbiota balance, characterized by reduced diversity and altered short-chain fatty acid (SCFA) production, is associated with IBD and its symptoms. Current pharmacological treatments target healing and remission, with vedolizumab offering a gut-selective treatment approach. Methods: A search of the literature was performed on the relationship between anti-integrin treatment and the microbiome profile in IBD. Articles were examined from the PubMed, Medline, Cochrane, and Web of Science databases. Results: This review identified five human studies investigating the relationship between gut microbiome composition, SCFAs, and response to vedolizumab, revealing an increased abundance of beneficial bacteria and levels of SCFAs like butyrate in remission cases. Despite promising findings, the small sample sizes and limited scope of the existing studies highlight the need for larger, comprehensive research. Conclusions: This review underscores the potential of gut microbiome and metabolite profiling as non-invasive biomarkers for IBD severity and treatment outcomes, advocating for personalized therapeutic strategies to enhance efficacy. The insights gained could lead to novel diagnostic and treatment modalities, although further validation is necessary to fully understand the intricate connections between gut microbiota and IBD prognosis.},
}

@article {pmid40284452,
year = {2025},
author = {Shi, T and Li, H and Zhang, Z and Zang, Y and Jiang, S and Yuan, T},
title = {The Effect of Gut Microbiome Perturbation on the Bioavailability of Glycyrrhizic Acid in Rats.},
journal = {Pharmaceutics},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics17040457},
pmid = {40284452},
issn = {1999-4923},
support = {81703396 and 81773837//National Natural Science Foundation of China/ ; },
abstract = {Background: Oral administration remains the most common route for drug absorption. Emerging evidence highlights the important role of gut microbiome in the pharmacokinetics of oral medications. Glycyrrhizic acid (GL), a widely used hepatoprotective drug, is orally administrated and subsequently biotransformed by the gut microbiota into its active metabolite, glycyrrhetinic acid (GA), which exerts a therapeutic effect. However, it remains unclear whether the disturbance of the gut microbiome directly impacts the metabolism of GL. Methods: Antibiotic cocktail and probiotic Lacticaseibacillus rhamnosus R0011 were applied as two interventions targeting the gut microbiome. Pharmacokinetic parameters were evaluated by LC-MS, and 16S rRNA sequencing was applied to analyze the gut microbiome composition. The transcriptome analysis of Caco-2 cells was used to elucidate the regulation mechanism of polar metabolites resulting from gut microbiome perturbation. Results: R0011 supplementation could significantly increase the Area Under Curve (AUC) value of GA, which was positively correlated with the change in gut microbiome composition. In contrast, the plasma levels of GA were nearly undetectable following antibiotic intervention. Furthermore, the relative expressions of transporter multidrug resistance gene 1 (MDR1) in the ileum were site specifically downregulated under the probiotic intervention. The polar gut microbial metabolites may play a crucial role in differentiated regulating MDR1 expression, likely through the modulation of transcription factors FoxO1 and TP53. Conclusions: Our research provides new insights into the regulatory mechanism by which the gut microbiome affects the bioabsorption of orally administrated drugs, potentially offering strategies to optimize drug bioavailability and improve clinical efficacy.},
}

@article {pmid40284263,
year = {2025},
author = {Pfäffle, SP and Herz, C and Brombacher, E and Proietti, M and Gigl, M and Hofstetter, CK and Mittermeier-Kleßinger, VK and Claßen, S and Tran, HTT and Rajguru, D and Dawid, C and Kreutz, C and Günther, S and Lamy, E},
title = {Correction: Pfäffle et al. A 14-Day Double-Blind, Randomized, Controlled Crossover Intervention Study with Anti-Bacterial Benzyl Isothiocyanate from Nasturtium (Tropaeolum majus) on Human Gut Microbiome and Host Defense. Nutrients 2024, 16, 373.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081367},
pmid = {40284263},
issn = {2072-6643},
abstract = {Dhairya Rajguru was not included as an author in the original publication [...].},
}

@article {pmid40284255,
year = {2025},
author = {San Diego, L and Hogue, T and Hampton-Marcell, J and Carroll, IM and Purdom, T and Colleran, H and Cook, MD},
title = {Gut Butyrate Reduction in Blood Pressure Is Associated with Other Vegetables, Whole Fruit, Total Grains, and Sodium Intake.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081392},
pmid = {40284255},
issn = {2072-6643},
support = {# 550KR181802//North Carolina Translational and Clinical Sciences (NC TraCS)/ ; 18CDA34110444//American Heart Association/ ; },
mesh = {Humans ; *Blood Pressure/drug effects ; Male ; *Gastrointestinal Microbiome/drug effects/physiology ; *Butyrates/administration & dosage/pharmacology/metabolism ; Middle Aged ; Adult ; Female ; *Vegetables ; *Hypertension/physiopathology/drug therapy/diet therapy ; *Whole Grains ; *Fruit ; Black or African American ; *Sodium, Dietary/administration & dosage ; Diet ; White ; },
abstract = {BACKGROUND: African Americans (AA) are disproportionally affected by hypertension (HTN). Gut microbiome metabolites (e.g., butyrate) may mediate the relationship between the microbiome and blood pressure (BP). Previous research reports a consistent indirect relationship between gut butyrate, a product of gut microbial nutrient fermentation, and BP. Thus, this study assessed the relationship between individual diet intake on BP changes after a butyrate treatment.

METHODS: AA aged 30-50 with HTN underwent treatment with a blinded placebo (5 mmol) and butyrate enema (80 mmol) with a one-week washout period. Ambulatory BP monitors collected measures up to 24 h post-enema. The Nutrition Data System for Research was used to assess diet and Healthy Eating Index (HEI-2015) scores from diet records. Paired t-tests and Kendall's correlation tests determined group differences and relationships between variables (p < 0.05).

RESULTS: Positive correlations were found between other vegetables and 24 h diastolic BP (r = 0.64), daytime diastolic BP (r = 0.68), and MAP (r = 0.72). Positive correlations were also found between 24 h systolic BP and HEI-2015 greens and beans sub-scores (r = 0.64) and 24 h DBP and total vegetables (r = 0.64). Negative correlations were found between nighttime arterial stiffness and total grain intake (r = -0.71).

CONCLUSION: These data suggest diet impacts BP measures in response to acutely increasing gut butyrate. These results provide preliminary evidence linking food groups, not individual nutrients, with BP outcomes and gut butyrate availability.},
}

Humans
*Blood Pressure/drug effects
Male
*Gastrointestinal Microbiome/drug effects/physiology
*Butyrates/administration & dosage/pharmacology/metabolism
Middle Aged
Adult
Female
*Vegetables
*Hypertension/physiopathology/drug therapy/diet therapy
*Whole Grains
*Fruit
Black or African American
*Sodium, Dietary/administration & dosage
Diet
White

@article {pmid40284246,
year = {2025},
author = {Sun, X and Li, W and Chen, G and Hu, G and Jia, J},
title = {Faecalibacterium duncaniae Mitigates Intestinal Barrier Damage in Mice Induced by High-Altitude Exposure by Increasing Levels of 2-Ketoglutaric Acid.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081380},
pmid = {40284246},
issn = {2072-6643},
support = {52104003 and 51110656//Foundation of Shenyang Pharmaceutical University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Ketoglutaric Acids/metabolism ; Male ; *Probiotics/pharmacology ; *Altitude ; *Intestinal Mucosa/metabolism/pathology/microbiology ; Apoptosis ; Humans ; Disease Models, Animal ; Occludin/metabolism ; },
abstract = {Background/Objectives: Exposure to high altitudes often results in gastrointestinal disorders. This study aimed to identify probiotic strains that can alleviate such disorders. Methods: We conducted a microbiome analysis to investigate the differences in gut microbiota among volunteers during the acute response and acclimatization phases at high altitudes. Subsequently, we established a mouse model of intestinal barrier damage induced by high-altitude exposure to further investigate the roles of probiotic strains and 2-ketoglutaric acid. Additionally, we performed untargeted metabolomics and transcriptomic analyses to elucidate the underlying mechanisms. Results: The microbiome analysis revealed a significant increase in the abundance of Faecalibacterium prausnitzii during the acclimatization phase. Faecalibacterium duncaniae (F. duncaniae) significantly mitigated damage to the intestinal barrier and the reduction of 2-ketoglutaric acid levels in the cecal contents induced by high-altitude exposure in mice. Immunohistochemistry and TUNEL staining demonstrated that high-altitude exposure significantly decreased the expression of ZO-1 and occludin while increasing apoptosis in ileal tissues. In contrast, treatment with F. duncaniae alleviated the loss of ZO-1 and occludin, as well as the apoptosis induced by high-altitude exposure. Furthermore, 2-ketoglutaric acid also mitigated this damage, reducing the loss of occludin and apoptosis in mice. Transcriptomic analysis indicated that high-altitude exposure significantly affects the calcium signaling pathway; conversely, the administration of F. duncaniae significantly influenced the PPAR signaling pathway, mineral absorption, and the regulation of lipolysis in adipocytes. Additionally, the expression of the FBJ osteosarcoma oncogene (Fos) was markedly reduced following the administration of F. duncaniae. Conclusions:F. duncaniae mitigates hypoxia-induced intestinal barrier damage by increasing levels of 2-ketoglutaric acid and shows promise as a probiotic, ultimately aiding travelers in adapting to high-altitude environments.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Ketoglutaric Acids/metabolism
Male
*Probiotics/pharmacology
*Altitude
*Intestinal Mucosa/metabolism/pathology/microbiology
Apoptosis
Humans
Disease Models, Animal
Occludin/metabolism

@article {pmid40284229,
year = {2025},
author = {Soliman, N and Kruithoff, C and San Valentin, EM and Gamal, A and McCormick, TS and Ghannoum, M},
title = {Small Intestinal Bacterial and Fungal Overgrowth: Health Implications and Management Perspectives.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081365},
pmid = {40284229},
issn = {2072-6643},
mesh = {Humans ; *Intestine, Small/microbiology ; *Gastrointestinal Microbiome ; *Blind Loop Syndrome/diagnosis/therapy/microbiology ; Dysbiosis ; Risk Factors ; *Fungi/growth & development ; *Bacteria/growth & development ; },
abstract = {BACKGROUND/OBJECTIVES: Small Intestinal Bacterial Overgrowth (SIBO) and Small Intestinal Fungal Overgrowth (SIFO) are distinct yet often overlapping conditions characterized by an abnormal increase in microbial populations within the small intestine. SIBO results from an overgrowth of colonic bacteria, while SIFO is driven by fungal overgrowth, primarily involving Candida species. Both conditions present with nonspecific gastrointestinal (GI) symptoms such as bloating, abdominal pain, diarrhea, and malabsorption, making differentiation between SIBO and SIFO challenging. This review aims to elucidate the underlying mechanisms, risk factors, diagnostic challenges, and management strategies associated with SIBO and SIFO.

METHODS: A comprehensive review of current literature was conducted, focusing on the pathophysiology, diagnostic modalities, and therapeutic approaches for SIBO and SIFO.

RESULTS: SIBO is commonly associated with factors such as reduced gastric acid secretion, impaired gut motility, and structural abnormalities like bowel obstruction and diverticula. It is frequently diagnosed using jejunal aspirates (≥10[5] colony forming units (CFUs)/mL) or breath tests. In contrast, SIFO is linked to prolonged antibiotic use, immunosuppression, and gut microbiome dysbiosis, with diagnosis relying on fungal cultures from small intestinal aspirates due to the absence of standardized protocols.

CONCLUSION: The clinical overlap and frequent misdiagnosis of SIBO and SIFO highlight the need for improved diagnostic tools and a multidisciplinary approach to management. This review emphasizes the importance of understanding the mechanisms behind SIBO and SIFO, how they relate to other health outcomes, and potential management strategies to optimize patient care and therapeutic outcomes.},
}

Humans
*Intestine, Small/microbiology
*Gastrointestinal Microbiome
*Blind Loop Syndrome/diagnosis/therapy/microbiology
Dysbiosis
Risk Factors
*Fungi/growth & development
*Bacteria/growth & development

@article {pmid40284216,
year = {2025},
author = {Oami, T and Yamamoto, A and Ishida, S and Kondo, K and Hata, N and Oshima, T},
title = {Critical Care Nutrition from a Metabolic Point of View: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081352},
pmid = {40284216},
issn = {2072-6643},
mesh = {Humans ; *Critical Illness/therapy ; *Gastrointestinal Microbiome/physiology ; *Critical Care/methods ; Dysbiosis ; Prebiotics/administration & dosage ; Probiotics ; *Nutrition Therapy/methods ; Inflammation ; },
abstract = {Background: Critical illness induces profound metabolic alterations, characterized by a hypermetabolic state, insulin resistance, protein catabolism, and gut barrier dysfunction, which contribute to increased morbidity and mortality. Emerging evidence highlights the role of the gut microbiome and its metabolites in modulating systemic inflammation and immune responses during critical illness. This narrative review explores the metabolic evolution of critically ill patients, the impact of gut dysbiosis on disease progression, and the potential role of nutrition in modulating metabolism and improving patient outcomes. Methods: A comprehensive literature search was conducted across PubMed and Google Scholar for articles published up to February 2025. Search terms included "critical illness", "metabolism", "gut microbiota", "nutrition", and related keywords. Articles published in English addressing metabolic alterations, microbiome changes, and nutritional strategies in critically ill patients were included. After screening for eligibility, relevant articles were synthesized to outline current knowledge and identify gaps. Results: Metabolic changes in critical illness progress through distinct phases, from catabolism-driven hypermetabolism to gradual recovery. Gut dysbiosis, characterized by a loss of microbial diversity and increased gut permeability, contributes to systemic inflammation and organ dysfunction. Nutritional strategies, including enteral nutrition, probiotics, prebiotics, and metabolomics-driven interventions, may help restore microbial balance, preserve gut barrier integrity, and modulate immune and metabolic responses. Future nutrition therapy should focus on metabolic modulation rather than solely addressing nutrient deficits. Conclusions: Advances in gut microbiome research and metabolomics offer new avenues for personalized nutrition strategies tailored to the metabolic demands of critically ill patients. Integrating these approaches may improve clinical and functional recovery while mitigating the long-term consequences of critical illness.},
}

Humans
*Critical Illness/therapy
*Gastrointestinal Microbiome/physiology
*Critical Care/methods
Dysbiosis
Prebiotics/administration & dosage
Probiotics
*Nutrition Therapy/methods
Inflammation

@article {pmid40284204,
year = {2025},
author = {Liu, S and Lin, Z and Huang, Z and Yu, M and Lin, Z and Hu, Z},
title = {Unique Microbial Characterisation of Oesophageal Squamous Cell Carcinoma Patients with Different Dietary Habits Based on Light Gradient Boosting Machine Learning Classifier.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081340},
pmid = {40284204},
issn = {2072-6643},
support = {82473698; 2019L3006 and 2020L3009; 23SCZZX004; 2021J01726 and 2021J01733//National Natural Science Foundation of China; the Central government-led local science and technology development special projec; the Fujian Provincial Financial Special Project; the Natural Science Foundation of Fujian Province/ ; },
mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/microbiology ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Middle Aged ; *Machine Learning ; RNA, Ribosomal, 16S/genetics ; *Feeding Behavior ; Aged ; Bacteria/classification/genetics ; *Microbiota ; Diet ; *Gastrointestinal Microbiome ; Boosting Machine Learning Algorithms ; },
abstract = {Objectives: The microbiome plays an important role in cancer, but the relationship between dietary habits and the microbiota in oesophageal squamous cell carcinoma (ESCC) is not clear. The aim of this study is to explore the complex relationship between the microbiota in oesophagal tissue and dietary habits in ESCC patients. Methods: 173 ESCC patients were included. The method of 16S rRNA sequencing was used to analyze microbial composition and diversity. The LEfSe and Boruta methods were used to screen important microbes, and the LightGBM algorithm distinguished microbes associated with different dietary habits. PICRUST2 and DESeq2 predicted microbial function and screened differential functions. The Pearson test was used to analyze correlations between microbes and functions, and SPARCC microbial symbiotic networks and Cytoscape were used to determine microbial interactions. Results: Significant differences in microbial composition were observed among ESCC patients with different dietary habits. LEfSe and Boruta identified three, six, and two significantly different bacteria in the FF/FP, FF/PF, and FF/PP groups, respectively, with AUC values of 0.683, 0.830, and 0.715. PICRUST2 and DESeq2 analysis revealed 3, 11, and 5 significantly different metabolic pathways in each group. Eubacterium_B sulci was positively correlated with PWY-6285, PWY-3801, and PWY-5823. PWY-6397 was positively correlated with undefinded (Fusobacterium_C). Microbial network analysis confirmed unique microbial characteristics in different diet groups. Conclusions: Different dietary habits lead to alterations in Eubacterium_B sulci and undefinded (Fusobacterium_C) and related functional pathways.},
}

Humans
*Esophageal Squamous Cell Carcinoma/microbiology
*Esophageal Neoplasms/microbiology
Male
Female
Middle Aged
*Machine Learning
RNA, Ribosomal, 16S/genetics
*Feeding Behavior
Aged
Bacteria/classification/genetics
*Microbiota
Diet
*Gastrointestinal Microbiome
Boosting Machine Learning Algorithms

@article {pmid40284194,
year = {2025},
author = {Thatrimontrichai, A and Praditaukrit, M and Maneenil, G and Dissaneevate, S and Singkhamanan, K and Surachat, K},
title = {Butyrate Producers in Very Low Birth Weight Infants with Neither Culture-Proven Sepsis nor Necrotizing Enterocolitis.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081329},
pmid = {40284194},
issn = {2072-6643},
support = {REC. 60-455-01-1//Prince of Songkla University/ ; },
mesh = {Humans ; *Infant, Very Low Birth Weight ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; *Enterocolitis, Necrotizing/microbiology ; Male ; Female ; *Sepsis/microbiology ; *Butyrates/metabolism ; Bacteria/metabolism/classification ; },
abstract = {Background/Objectives: Severe infection (sInfection; either late-onset culture-proven sepsis or necrotizing enterocolitis) in very low birth weight (VLBW) infants increases mortality rates and may show long-term progression. The fecal microbiome composition in VLBW infants with and without sInfection was classified in the sInfection and non-sInfection groups. Methods: Gut microbiomes, secondary information from a previous randomized trial, were analyzed using QIIME 2 software. The biodiversity and abundance of the gut microbiota between the sInfection and non-sInfection groups were compared. Results: Fifty-one neonates were included in the sInfection (n = 9) and non-sInfection (n = 42) groups; no significant differences in the fecal microbiome were observed in both alpha and beta diversities. Analysis of relative abundance revealed that in both groups, the predominant gut microbiota phylum, class, and genus were Proteobacteria, Gammaproteobacteria, and Klebsiella, respectively. The main fecal microbiome in the non-sInfection group included Faecalibacterium, Clostridium butyricum, and Bacteroides fragilis. Clostridium_sensu_stricto _1 was significantly more abundant in the non-sInfection group than in the sInfection group. Conclusions: Clostridium_sensu_stricto_1 was the main gut microbiota in the non-sInfection group. Considering the potential taxa as synbiotics (correlations among prebiotics, probiotics, and postbiotics), therapeutics may be useful for preventing and managing necrotizing enterocolitis or late-onset culture-proven sepsis in VLBW infants.},
}

Humans
*Infant, Very Low Birth Weight
*Gastrointestinal Microbiome
Infant, Newborn
Feces/microbiology
*Enterocolitis, Necrotizing/microbiology
Male
Female
*Sepsis/microbiology
*Butyrates/metabolism
Bacteria/metabolism/classification

@article {pmid40284188,
year = {2025},
author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G},
title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081323},
pmid = {40284188},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.},
}

Humans
*Arthritis, Psoriatic/microbiology/therapy/immunology
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid40284168,
year = {2025},
author = {Gofron, KK and Wasilewski, A and Małgorzewicz, S},
title = {Effects of GLP-1 Analogues and Agonists on the Gut Microbiota: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081303},
pmid = {40284168},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Animals ; *Glucagon-Like Peptide 1/analogs & derivatives/agonists/pharmacology ; Glucagon-Like Peptides/pharmacology/analogs & derivatives ; Exenatide/pharmacology ; *Hypoglycemic Agents/pharmacology ; Liraglutide/pharmacology ; Immunoglobulin Fc Fragments ; Recombinant Fusion Proteins ; },
abstract = {BACKGROUND: GLP-1 analogues are a relatively new class of medications that form the cornerstone of diabetes treatment. They possess invaluable glucose-lowering properties without hypoglycemic effects as well as strong cardioprotective effects. The gut microbiome has become the focus of numerous studies, demonstrating its influence not only on the gut but also on the overall well-being of the entire body. However, the effects of GLP-1 analogs on gut microbiota remain uncertain.

SCOPE OF REVIEW: Our systematic review (based on PRISMA guidelines) aimed to gather knowledge on the effects of GLP-1 analogue medications on the composition, richness, and abundance of gut microbiota in both animal and human models.

CONCLUSIONS: Thirty-eight studies were included in this systematic review. GLP-1 analogues have demonstrated a notable impact on the composition, richness, and diversity of gut microbiota. We can conclude, following the obtained research results of our study, that liraglutide promotes the growth of beneficial genera relevant for beneficial metabolic functions. Exenatide and exendin-4 administration showed various effects on the microbiome composition in animal and human studies. In animal models, it increased genera associated with improved metabolism; however, in human models, genera linked to better metabolic functions and escalated inflammation increased. Following dulaglutide administration, increases in Bacteroides, Akkermansia, and Ruminococcus, genera connected to an improved metabolic model, were significant. Finally, varied results were obtained after semaglutide treatment, in which A. muciniphila, known for its positive metabolic functions, increased; however, microbial diversity decreased. Semaglutide treatment provided various results indicating many confounding factors in semaglutide's impact on the gut microbiota. Results varied due to dissimilarities in the studied populations and the duration of the studies. Further research is essential to confirm these findings and to better recognize their implications for the clinical outcomes of patients.},
}

*Gastrointestinal Microbiome/drug effects
Humans
Animals
*Glucagon-Like Peptide 1/analogs & derivatives/agonists/pharmacology
Glucagon-Like Peptides/pharmacology/analogs & derivatives
Exenatide/pharmacology
*Hypoglycemic Agents/pharmacology
Liraglutide/pharmacology
Immunoglobulin Fc Fragments
Recombinant Fusion Proteins

@article {pmid40284136,
year = {2025},
author = {Buirs, L and Punja, ZK},
title = {Endophytes in Cannabis sativa: Identifying and Characterizing Microbes with Beneficial and Detrimental Effects on Plant Health.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/plants14081247},
pmid = {40284136},
issn = {2223-7747},
support = {ALLRP 571270-21//Natural Sciences and Engineering Research Council/ ; 31-832855//Pure Sunfarms/ ; },
abstract = {The roles of endophytes in Cannabis sativa (cannabis, hemp) remain poorly explored. While in vitro studies suggest that there can be several benefits, such as plant growth promotion and protection against pathogens, more in planta studies are needed. This review summarizes the bacterial and fungal endophytes previously reported in tissues of C. sativa and discusses the factors influencing their presence, as well as their potential beneficial and detrimental effects. Using genome sequencing and culture-based approaches, we describe the microbial diversity in hydroponically cultivated cannabis plants at several developmental stages. These include mother plants, cuttings, vegetative and flowering plants, and tissue-cultured plantlets. Microbes that were present include fungal, yeast, and bacterial endophytes found in roots, stems, leaves, inflorescences, and seeds. These may have originated from the growing substrate or be transmitted through vegetative propagation. Notable endophytes included Rhizophagus irregularis (a mycorrhizal fungus), Penicillium chrysogenum (an antibiotic producer), and various endophytic yeast species not previously described in C. sativa. Endophytes representing potential plant pathogens, such as Fusarium oxysporum, are also present within cannabis tissues, which can negatively impact plant health. Using scanning electron microscopy, we observed that fungal propagules are present within pith parenchyma cells and xylem vessel elements in stem tissues, illustrating for the first time the in situ localization and distribution of endophytes in cannabis vascular tissues. The mechanism of spread through xylem vessels likely contributes to the spread of endophytes within cannabis and hemp plants. Further research is required to validate the roles of endophytes in cannabis and hemp plants grown under commercial production conditions.},
}

@article {pmid40284077,
year = {2025},
author = {Sonam, W and Liu, Y and Ren, L},
title = {Differentiation and Interconnection of the Bacterial Community Associated with Silene nigrescens Along the Soil-To-Plant Continuum in the Sub-Nival Belt of the Qiangyong Glacier.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/plants14081190},
pmid = {40284077},
issn = {2223-7747},
support = {42330410//The National Natural Science Foundation of China/ ; 2019QZKK0503//National Natural Science Foundation of China/ ; },
abstract = {Plant microbiomes provide significant fitness advantages to their plant hosts, especially in the sub-nival belt. Studies to date have primarily focused on belowground communities in this region. Here, we utilized high-throughput DNA sequencing to quantify bacterial communities in the rhizosphere soil as well as in the root and leaf endosphere compartments of Silene nigrescens to uncover the differentiation and interconnections of these bacterial communities along the soil-to-plant continuum. Our findings reveal that the bacterial communities exhibit notable variation across different plant compartment niches: the rhizosphere soil, root endosphere, and leaf endosphere. There was a progressive decline in diversity, network complexity, network modularity, and niche breadth from the rhizosphere soil to the root endosphere, and further to the leaf endosphere. Conversely, both the host plant selection effect and the stability of these communities showed an increasing trend. Total nitrogen and total potassium emerged as crucial factors accounting for the observed differences in diversity and composition, respectively. Additionally, 3.6% of the total amplicon sequence variants (ASVs) were shared across the rhizosphere soil, root endosphere, and leaf endosphere. Source-tracking analysis further revealed bacterial community migration among these compartments. The genera Pseudomonas, IMCC26256, Mycobacterium, Phyllobacterium, and Sphingomonas constituted the core of the bacterial microbiome. These taxa are shared across all three compartment niches and function as key connector species. Notably, Pseudomonas stands out as the predominant taxon among these bacteria, with nitrogen being the most significant factor influencing its relative abundance. These findings deepen our understanding of the assembly principles and ecological dynamics of the plant microbiome in the sub-nival belt, offering an integrated framework for its study.},
}

@article {pmid40283951,
year = {2025},
author = {Oglio, F and Coppola, S and Agizza, A and Masino, A and Luongo, C and Di Santillo, R and D'Auria, L and Russo, R and Neri, I and Grumetto, L and Carucci, L and Caldaria, E and Nocerino, R and Di Lorenzo, R and Calignano, A and Laneri, S and Paparo, L and Berni Canani, R},
title = {The Beneficial Effects of a N-(1-Carbamoyl-2-phenyl-ethyl) Butyramide on Human Keratinocytes.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/ph18040517},
pmid = {40283951},
issn = {1424-8247},
abstract = {Background: The skin microbiota-derived metabolite butyrate plays a pivotal role in maintaining skin health. Unfortunately, unpleasant sensorial properties and unfavorable physicochemical properties strongly limit the butyrate use in dermatology clinical practice. This study investigates the effects of N-(1-carbamoyl-2-phenyl-ethyl) butyramide (FBA), a butyric acid releaser with neutral sensorial properties on skin keratinocyte function. Methods: Immortalized human keratinocyte cell line (HaCaT cells) was treated with FBA at various concentrations (0.001-1 mM) and time points (6-48 h). Cellular proliferation was assessed using MTT assays, while barrier integrity was evaluated by measuring tight junction proteins (occludin and ZO-1). Oxidative stress was analyzed using ROS assays and Western blot for Nrf2 and NF-κB expression. Markers of differentiation and extracellular matrix proteins were measured via quantitative PCR and wound-healing capability was assessed using a scratch assay. Results: FBA significantly enhanced keratinocyte proliferation at an optimal concentration of 0.1 mM. Tight junction protein expression increased, indicating improved barrier function. FBA reduced oxidative stress by upregulating Nrf2 and suppressing NF-κB activity. It also promoted the expression of differentiation markers (e.g., keratin-1, filaggrin) and extracellular matrix proteins (e.g., collagen type I and elastin). Furthermore, FBA accelerated wound closure, demonstrating its efficacy in enhancing the mechanisms of skin repair. Conclusions: Our results demonstrate that FBA enhances human keratinocyte cell differentiation, proliferation, and skin repair while protecting against oxidative stress. Its potential in cosmetics lies in delivering butyric acid benefits without organoleptic limitations, with possible applications in several skin condition characterized by deficient butyrate production and inflammation, such as atopic dermatitis.},
}

@article {pmid40283915,
year = {2025},
author = {Thapa, D and Ghimire, A and Warne, LN and Carlessi, R},
title = {Targeting the Endocannabinoidome: A Novel Approach to Managing Extraintestinal Complications in Inflammatory Bowel Disease.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/ph18040478},
pmid = {40283915},
issn = {1424-8247},
abstract = {Background: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder marked by persistent gastrointestinal inflammation and a spectrum of systemic effects, including extraintestinal manifestations (EIMs) that impact the joints, skin, liver, and eyes. Conventional therapies primarily target intestinal inflammation, yet they frequently fail to ameliorate these systemic complications. Recent investigations have highlighted the complex interplay among the immune system, gut, and nervous system in IBD pathogenesis, thereby underscoring the need for innovative therapeutic approaches. Methods: We conducted a comprehensive literature search using databases such as PubMed, Scopus, Web of Science, Science Direct, and Google Scholar. Keywords including "cannabinoids", "endocannabinoid system", "endocannabinoidome", "inflammatory bowel disease", and "extraintestinal manifestations" were used to identify peer-reviewed original research and review articles that explore the role of the endocannabinoidome (eCBome) in IBD. Results: Emerging evidence suggests that eCBome-a network comprising lipid mediators, receptors (e.g., CB1, CB2, GPR55, GPR35, PPARα, TRPV1), and metabolic enzymes-plays a critical role in modulating immune responses, maintaining gut barrier integrity, and regulating systemic inflammation. Targeting eCBome not only improves intestinal inflammation but also appears to mitigate metabolic, neurological, and extraintestinal complications such as arthritis, liver dysfunction, and dermatological disorders. Conclusions: Modulation of eCBome represents a promising strategy for comprehensive IBD management by addressing both local and systemic disease components. These findings advocate for further mechanistic studies to develop targeted interventions that leverage eCBome as a novel therapeutic avenue in IBD.},
}

@article {pmid40283730,
year = {2025},
author = {Sebothoma, B and Khoza-Shangase, K and Khumalo, G and Mokwena, B},
title = {Exploring Middle Ear Pathologies in Adults with Diabetes Mellitus: A Scoping Review of Available Evidence and Research Gaps.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {4},
pages = {},
doi = {10.3390/ijerph22040503},
pmid = {40283730},
issn = {1660-4601},
mesh = {Humans ; *Ear, Middle/pathology ; Adult ; *Diabetes Mellitus/epidemiology ; *Diabetes Complications/epidemiology ; Evidence Gaps ; },
abstract = {Diabetes mellitus (DM) is a common chronic health condition, affecting millions of people worldwide, and its incidence is projected to increase by almost 50% in the next two decades. The effects of DM on the auditory system have been reported. However, there is limited evidence on the association between DM and middle ear pathologies. This scoping review aimed to map the available evidence and identify research gaps regarding DM and middle ear pathologies in the adult population. Five electronic databases, namely Scopus, CINAHL, MEDLINE, PubMed, and Web of Science, were searched using a combination of specific key terms. This review followed the guidelines stipulated by the Joanna Briggs Institute (JBI) methodology for scoping reviews and reporting using PRISMA Extension for Scoping Reviews (PRISMA-ScR): checklist and explanation. A thematic narrative analysis was used to synthesize key findings. Of the 1809 articles, only 2 articles met the inclusion criteria. Neither of these studies focused exclusively on middle ear pathologies in DM, but they did report incidental findings related to middle ear function. Available evidence suggests that middle ear pathologies may occur in individuals with DM, with a reported prevalence ranging from 3.1% to 19.6%. Otitis media with effusion and conductive hearing loss were common middle ear pathologies identified. Additionally, recent studies have provided new evidence suggesting ossicular joint changes in individuals with DM and a causal link between DM and acute suppurative otitis media. However, age-related hearing loss (presbycusis) and sensorineural hearing loss (SNHL) were more commonly associated with DM, with studies reporting a high prevalence of SNHL in younger to middle-aged adults with diabetes. This review highlights a significant research gap in the literature, as no studies directly investigated the relationship between DM and middle ear function as a primary focus. Further research is required to investigate this potential association using methodologies explicitly designed for middle ear assessment. While some evidence suggests a possible association, the lack of age-stratified analyses, imaging data, and comprehensive diagnostic testing limits the ability to draw strong conclusions. Further research incorporating age-based analyses, radiological assessments, and microbiome studies is needed to fully understand the potential impact of DM on middle ear health.},
}

Humans
*Ear, Middle/pathology
Adult
*Diabetes Mellitus/epidemiology
*Diabetes Complications/epidemiology
Evidence Gaps

@article {pmid40283154,
year = {2025},
author = {Plaza-Díaz, J and Fernández, MF and García, F and Chueca, N and Fontana, L and Álvarez-Mercado, AI},
title = {Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040599},
pmid = {40283154},
issn = {2075-1729},
support = {PI-0538-2017//Junta de Andalucía/ ; },
abstract = {Breast cancer is the most commonly diagnosed cancer in women and the second leading cause of female death. Altered interactions between the host and the gut microbiota appear to play an influential role in carcinogenesis. Several studies have shown different signatures of the gut microbiota in patients with breast cancer compared to healthy women. Currently, there is disagreement regarding the different DNA isolation and sequencing methodologies for studies on the human microbiota, given that they can influence the interpretation of the results obtained. The goal of this work was to compare (1) three different DNA extraction strategies to minimize the impact of human DNA, and (2) two sequencing strategies (16S rRNA and shotgun) to identify discrepancies in microbiome results. We made use of breast tissue and fecal samples from both healthy women and breast cancer patients who participated in the MICROMA study (reference NCT03885648). DNA was isolated by means of mechanical lysis, trypsin, or saponin. The amount of eukaryotic DNA isolated using the trypsin and saponin methods was lower compared to the mechanical lysis method (mechanical lysis, 89.11 ± 2.32%; trypsin method, 82.63 ± 1.23%; saponin method, 80.53 ± 4.09%). In samples with a predominance of prokaryotic cells, such as feces, 16S rRNA sequencing was the most advantageous approach. For other tissues, which are expected to have a more complex microbial composition, the need for an in-depth evaluation of the multifactorial interaction between the various components of the microbiota makes shotgun sequencing the most appropriate method. As for the three extraction methods evaluated, when sequencing samples other than stool, the trypsin method is the most convenient. For fecal samples, where contamination by host DNA is low, no prior treatment is necessary.},
}

@article {pmid40283148,
year = {2025},
author = {Marano, G and Rossi, S and Sfratta, G and Traversi, G and Lisci, FM and Anesini, MB and Pola, R and Gasbarrini, A and Gaetani, E and Mazza, M},
title = {Gut Microbiota: A New Challenge in Mood Disorder Research.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040593},
pmid = {40283148},
issn = {2075-1729},
abstract = {The gut microbiome has emerged as a novel and intriguing focus in mood disorder research. Emerging evidence demonstrates the significant role of the gut microbiome in influencing mental health, suggesting a bidirectional communication between the gut and the brain. This review examines the latest findings on the gut-microbiota-brain axis and elucidates how alterations in gut microbiota composition can influence this axis, leading to changes in brain function and behavior. Although dietary interventions, prebiotics, probiotics, and fecal microbiota transplantation have yielded encouraging results, significant advances are needed to establish next-generation approaches that precisely target the neurobiological mechanisms of mood disorders. Future research must focus on developing personalized treatments, facilitated by innovative therapies and technological progress, which account for individual variables such as age, sex, drug history, and lifestyle. Highlighting the potential therapeutic implications of targeting the gut microbiota, this review emphasizes the importance of integrating microbiota research into psychiatric studies to develop more effective and personalized treatment strategies for mood disorders.},
}

@article {pmid40283043,
year = {2025},
author = {Nam, G and Lee, KA and Kim, SJ and Oh, KY and Lee, S and Lee, HC and Kim, SY and Park, MH},
title = {A Comparative Longitudinal Study Analyzing Vaginal Microbiota Differences Between Term and Preterm Pregnancies in Korean Women.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {4},
pages = {},
doi = {10.3390/medicina61040752},
pmid = {40283043},
issn = {1648-9144},
support = {RS-2023-00281006//National Research Foundation of Korea, Ministry of Science and ICT/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Vagina/microbiology ; Adult ; Longitudinal Studies ; *Premature Birth/microbiology ; Republic of Korea ; *Microbiota/physiology ; Cohort Studies ; },
abstract = {Background and Objectives: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, remains a significant public health concern due to its association with neonatal morbidity and mortality. Although studies have suggested that microbial factors in vaginal microbiota (VMB) influence PTB, longitudinal research on Korean women is limited. This study aimed to analyze VMB differences between term and preterm pregnancies in Korean women and their correlation with the cervical length (CL). Materials and Methods: A cohort of 60 pregnant Korean women (40 who had a term birth (TB) and 20 who had a PTB) was recruited. Vaginal samples were collected at five time points (first, second, and third trimester; 1-2 weeks postpartum; 1-2 months postpartum). Microbial DNA was extracted and analyzed using quantitative PCR targeting 12 bacterial species. The CL was measured in the second and third trimesters. Results: Lactobacillus crispatus was consistently dominant in the TB group, whereas PTB cases exhibited greater microbial diversity with elevated levels of Prevotella salivae and Ureaplasma species. The CL was significantly shorter in PTB cases, correlating with shifts in the VMB composition. Conclusions: A stable, Lactobacillus-dominant microbiome is protective in pregnancy, while increased diversity in PTB cases suggests microbial biomarkers for early risk prediction. Combining VMB profiling with CL measurement may enhance early, non-invasive PTB risk assessments.},
}

Humans
Female
Pregnancy
*Vagina/microbiology
Adult
Longitudinal Studies
*Premature Birth/microbiology
Republic of Korea
*Microbiota/physiology
Cohort Studies

@article {pmid40282690,
year = {2025},
author = {Bolino, M and Haththotuwe Gamage, N and Duman, H and Abiodun, O and De Mello, AS and Karav, S and Frese, SA},
title = {Novel Endo-β-N-Acetylglucosaminidases Derived from Human Fecal Samples Selectively Release N-Glycans from Model Glycoproteins.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081288},
pmid = {40282690},
issn = {2304-8158},
support = {GM103440/GM/NIGMS NIH HHS/United States ; GM104944/GM/NIGMS NIH HHS/United States ; 13385133//USDA NIFA/ ; },
abstract = {Three novel endo-β-N-acetylglucosaminidases (AVUL01, BCAC01, and BFIN01) classified as members of the glucoside hydrolase (GH) family 18 were identified from human fecal samples and then cloned and characterized for their ability to hydrolyze two distinct classes of N-glycans. Endo-β-N-acetylglucosaminidases (ENGases) are known for the hydrolysis of chitin and the N,N'-diacetylchitobiose core of N-linked glycans, depending on the glycan architecture. N-glycans have shown bioactivity as substrates in the human gut microbiome for microbes that encode ENGases, thus demonstrating their ecological relevance in the gut. However, distinct types of N-glycan structures, for example, oligomannosidic or complex, have been shown to enrich different microbes within the human gut. Novel advances in food technology have commercialized animal-derived dietary proteins with oligomannosidic instead of traditionally complex N-glycans using precision fermentation. This indicates that there is an unmet need to identify the classes of N-glycans that gut-derived ENGases act upon to determine whether these novel proteins alter gut ecology. AVUL01, BCAC01, and BFIN01 all demonstrated activity on exclusively oligomannosidic N-glycans from RNase B and bovine lactoferrin; however, they failed to show activity on complex or α-1,3-core fucosylated high-mannose N-glycans derived from fetuin and horseradish peroxidase, respectively. These results suggest that α-1,3 core fucosylation and complex N-glycan architecture inhibit the activity of AVUL01, BCAC01, and BFIN01. Furthermore, BFIN01 performed significantly better than BCAC01, resulting in a greater amount of N-glycans, suggesting that certain ENGases may possess enhanced specificity and kinetics as an evolutionary strategy to compete for resources.},
}

@article {pmid40282458,
year = {2025},
author = {Yun, J and Song, JS and Yoo, JJ and Kweon, S and Choi, YY and Lim, D and Kuk, JC and Kim, HJ and Park, SK},
title = {Microbial and Immune Landscape of Malignant Ascites: Insights from Gut, Bladder, and Ascitic Fluid Analyses.},
journal = {Cancers},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/cancers17081280},
pmid = {40282458},
issn = {2072-6694},
support = {NRF-2021R1G1A1010833//the Ministry of Education of the Republic of Korea/ ; NRF-2021R1G1A1007886//National Research Foundation of Korea/ ; 2025//Soonchunhyang University/ ; },
abstract = {BACKGROUND/OBJECTIVES: Malignant ascites frequently arises in advanced cancers with peritoneal metastasis and is associated with poor outcomes. Known mechanisms include lymphatic obstruction by tumor cells, increased vascular permeability, and sodium retention via the renin-angiotensin-aldosterone system; however, the pathogenesis remains not fully understood. We investigated whether gut and bladder microbiomes correlate with malignant ascites development or progression and whether the immune microenvironment in ascitic fluid is altered.

METHODS: We enrolled 66 histologically confirmed cancer patients, dividing them into malignant ascites (n = 20) and non-ascites (n = 46) groups. Stool, urine, and ascitic fluid samples were analyzed using 16S rRNA next-generation sequencing. Immune cell subsets in ascitic fluid were characterized using flow cytometry.

RESULTS: In 19 of the 20 malignant ascites samples, the bacterial load was too low for reliable 16S rRNA sequencing, suggesting that malignant ascites is largely sterile. The overall gut microbiome diversity did not differ significantly by ascites status, although a trend emerged in patients with peritoneal metastasis, including the enrichment of class Clostridia and Gammaproteobacteria. Bladder microbiome analysis also showed no significant differences in ascites or metastasis status. Flow cytometry revealed reduced T-cell (CD3+, CD4+, CD8+) and NK cell (CD56+) populations compared to data from cirrhotic ascites.

CONCLUSIONS: Malignant ascites exhibit minimal bacterial biomass, making comprehensive microbiome analysis challenging. Although no major global changes were noted in gut and bladder microbiomes, specific taxa were linked to peritoneal metastasis. These findings highlight an immunosuppressive ascitic environment and suggest that larger-scale or multi-omics approaches may help elucidate the role of microbiota in malignant ascites.},
}

@article {pmid40282413,
year = {2025},
author = {Han, H and Li, Y and Qi, Y and Mangiola, S and Ling, W},
title = {Deciphering Gut Microbiome in Colorectal Cancer via Robust Learning Methods.},
journal = {Genes},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/genes16040452},
pmid = {40282413},
issn = {2073-4425},
support = {R01 GM151301/GM/NIGMS NIH HHS/United States ; R01 GM155734/GM/NIGMS NIH HHS/United States ; R01 HL155417/HB/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; *Machine Learning ; Case-Control Studies ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent cancers worldwide and is closely linked to the gut microbiota. Identifying reproducible and generalizable microbial signatures holds significant potential for enhancing early detection and advancing treatment for this deadly disease.

METHODS: This study integrated various publicly available case-control datasets to identify microbial signatures for CRC. Alpha and beta diversity metrics were evaluated to characterize differences in gut microbial richness, evenness, and overall composition between CRC patients and healthy controls. Differential abundance analysis was conducted using ANCOM-BC and LEfSe to pinpoint individual taxa that were enriched or depleted in CRC patients. Additionally, sccomp, a Bayesian machine learning method from single-cell analysis, was adapted to provide a more robust validation of compositional differences in individual microbial markers.

RESULTS: Gut microbial richness is significantly higher in CRC patients, and overall microbiome composition differs significantly between CRC patients and healthy controls. Several taxa, such as Fusobacterium and Peptostreptococcus, are enriched in CRC patients, while others, including Anaerostipes, are depleted. The microbial signatures identified from the integrated data are reproducible and generalizable, with many aligning with findings from previous studies. Furthermore, the use of sccomp enhanced the precision of individual microbial marker identification.

CONCLUSIONS: Biologically, the microbial signatures identified from the integrated data improve our understanding of the gut microbiota's role in CRC pathogenesis and may contribute to the development of translational targets and microbiota-based therapies. Methodologically, this study demonstrates the effectiveness of adapting robust techniques from single-cell research to improve the precision of microbial marker discovery.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
*Machine Learning
Case-Control Studies

@article {pmid40282363,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {Pharmacogenomic and Pharmacomicrobiomic Aspects of Drugs of Abuse.},
journal = {Genes},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/genes16040403},
pmid = {40282363},
issn = {2073-4425},
mesh = {Humans ; *Substance-Related Disorders/genetics/drug therapy/microbiology ; *Pharmacogenetics/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; *Illicit Drugs/pharmacokinetics ; },
abstract = {BACKGROUND/OBJECTIVES: This review examines the role of pharmacogenomics in individual responses to the pharmacotherapy of various drugs of abuse, including alcohol, cocaine, and opioids, to identify genetic variants that contribute to variability in substance use disorder treatment outcomes. In addition, it explores the pharmacomicrobiomic aspects of substance use, highlighting the impact of the gut microbiome on bioavailability, drug metabolism, pharmacodynamics, and pharmacokinetics.

RESULTS: Research on pharmacogenetics has identified several promising genetic variants that may contribute to the individual variability in responses to existing pharmacotherapies for substance addiction. However, the interpretation of these findings remains limited. It is estimated that genetic factors may account for 20-95% of the variability in individual drug responses. Therefore, genetic factors alone cannot fully explain the differences in drug responses, and factors such as gut microbiome diversity may also play a significant role. Drug microbial biotransformation is produced by microbial exoenzymes that convert low molecular weight organic compounds into analogous compounds by oxidation, reduction, hydrolysis, condensation, isomerization, unsaturation, or by the introduction of heteroatoms. Despite significant advances in pharmacomicrobiomics, challenges persist including the lack of standardized methodologies, inter-individual variability, limited understanding of drug biotransformation mechanisms, and the need for large-scale validation studies to develop microbiota-based biomarkers for clinical use.

CONCLUSIONS: Progress in the pharmacogenomics of substance use disorders has provided biological insights into the pharmacological needs associated with common genetic variants in drug-metabolizing enzymes. The gut microbiome and its metabolites play a pivotal role in various stages of drug addiction including seeking, reward, and biotransformation. Therefore, integrating pharmacogenomics with pharmacomicrobiomics will form a crucial foundation for significant advances in precision and personalized medicine.},
}

Humans
*Substance-Related Disorders/genetics/drug therapy/microbiology
*Pharmacogenetics/methods
*Gastrointestinal Microbiome/genetics/drug effects
*Illicit Drugs/pharmacokinetics

@article {pmid40282362,
year = {2025},
author = {Parisi, GF and Terlizzi, V and Manti, S and Papale, M and Pecora, G and Presti, S and Tosto, M and Leonardi, S},
title = {Cutting-Edge Advances in Cystic Fibrosis: From Gene Therapy to Personalized Medicine and Holistic Management.},
journal = {Genes},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/genes16040402},
pmid = {40282362},
issn = {2073-4425},
mesh = {Humans ; *Cystic Fibrosis/therapy/genetics ; *Precision Medicine/methods ; *Genetic Therapy/methods ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; Quality of Life ; Mutation ; Holistic Health ; Gene Editing ; },
abstract = {Cystic fibrosis (CF), a genetic disorder characterized by mutations in the CFTR gene, has seen significant advances in treatment through cutting-edge approaches such as gene therapy and personalized medicine. This review examines the current and emerging strategies shaping CF care, focusing on novel therapies that target the root cause of CF and optimize patient outcomes. CFTR modulators have transformed cystic fibrosis management by enhancing protein function for specific mutations, leading to improved lung function and quality of life. Concurrently, gene therapy offers transformative potential by aiming to correct CFTR mutations using tools like CRISPR/Cas9 or prime editing, though challenges remain in delivery and long-term efficacy. The integration of precision medicine, facilitated by genomic and computational technologies, allows for personalized treatment plans that account for genetic variability and disease severity. Complementing these approaches, holistic management emphasizes the importance of psychological support and nutritional optimization, acknowledging CF's multi-system impact. Future directions include exploring anti-inflammatory agents and microbiome modulation to further mitigate disease morbidity. However, global disparities in treatment access continue to challenge equitable healthcare delivery, underscoring the need for policy reform and international cooperation. By synthesizing these developments, this review highlights the transformative potential of modern CF treatments, advocating for continued innovation and global healthcare equity, with the ultimate goal of dramatically improving life expectancy and quality of life for individuals with CF.},
}

Humans
*Cystic Fibrosis/therapy/genetics
*Precision Medicine/methods
*Genetic Therapy/methods
Cystic Fibrosis Transmembrane Conductance Regulator/genetics
Quality of Life
Mutation
Holistic Health
Gene Editing

@article {pmid40282300,
year = {2025},
author = {Nemati, MH and Yazdanpanah, E and Kazemi, R and Orooji, N and Dadfar, S and Oksenych, V and Haghmorad, D},
title = {Microbiota-Driven Mechanisms in Multiple Sclerosis: Pathogenesis, Therapeutic Strategies, and Biomarker Potential.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040435},
pmid = {40282300},
issn = {2079-7737},
abstract = {Multiple sclerosis (MS) is a well-known, chronic autoimmune disorder of the central nervous system (CNS) involving demyelination and neurodegeneration. Research previously conducted in the area of the gut microbiome has highlighted it as a critical contributor to MS pathogenesis. Changes in the commensal microbiota, or dysbiosis, have been shown to affect immune homeostasis, leading to elevated levels of pro-inflammatory cytokines and disruption of the gut-brain axis. In this review, we provide a comprehensive overview of interactions between the gut microbiota and MS, especially focusing on the immunomodulatory actions of microbiota, such as influencing T-cell balance and control of metabolites, e.g., short-chain fatty acids. Various microbial taxa (e.g., Prevotella and Faecalibacterium) were suggested to lay protective roles, whereas Akkermansia muciniphila was associated with disease aggravation. Interventions focusing on microbiota, including probiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary therapies to normalize gut microbial homeostasis, suppress inflammation and are proven to improve clinical benefits in MS patients. Alterations in gut microbiota represent opportunities for identifying biomarkers for early diagnosis, disease progression and treatment response monitoring. Further studies need to be conducted to potentially address the interplay between genetic predispositions, environmental cues, and microbiota composition to get the precise mechanisms of the gut-brain axis in MS. In conclusion, the gut microbiota plays a central role in MS pathogenesis and offers potential for novel therapeutic approaches, providing a promising avenue for improving clinical outcomes in MS management.},
}

@article {pmid40282294,
year = {2025},
author = {Jeong, J and Kim, J and Lee, B and Park, C and Kim, M},
title = {Effects of Low and High Doses of Deoxynivalenol on Growth Performance, Blood Biochemistry, Histology, Metabolites, and Microbial Community in Adult Rats.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040429},
pmid = {40282294},
issn = {2079-7737},
support = {Project No. PJ016800//This research was funded by the Cooperative Research Program for Agriculture, Science, and Technology Development (Project No. PJ016800), the Rural Development Administration, Republic of Korea/ ; },
abstract = {Deoxynivalenol (DON) is a widespread mycotoxin which contaminates several crops, including maize, wheat, and barley. In this study, we investigated the effects of orally administered DON on growth performance, blood biochemistry, histology, the gut microbiome, and metabolism in rats. Six-week-old rats, acclimatized for one week, were subjected to different dietary treatments for 42 days, as follows: CON (control): 0.9% saline; T1: 0.5 ppm DON; T2: 50 ppm DON; and T3: 100 ppm DON. The T3 group had the lowest final body weight (298.5 ± 3.69 g) and average daily gain compared with the control group (338.9 ± 6.43 g, p < 0.05). The feed conversion ratio was highest in the T3 group (4.28 ± 0.28) compared with that in the control group (3.12 ± 0.13, p < 0.05). DON treatment significantly reduced serum levels of creatinine, amylase, urea nitrogen, and alkaline phosphatase, but not alanine aminotransferase. Fibrosis and apoptosis were exacerbated in various tissues with increasing DON concentration. The metabolite profiles of several tissues were significantly different in the DON-treated and control groups. In the cecum, DON treatment increased the abundance of Desulfobacteria, while decreasing that of Firmicutes. Our results indicate that DON levels above the maximum residue limit have serious health consequences for animals.},
}

@article {pmid40282255,
year = {2025},
author = {Cavalcante, FG and Bandeira, LL and Faria, CMA and Mesquita, AFN and Matos Neto, JM and Martins, CM and Martins, SCS},
title = {The Unseen Impacts of Human Footprints: How Land Use Reshapes Actinobacterial Communities in the Brazilian Cerrado.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040390},
pmid = {40282255},
issn = {2079-7737},
support = {ICMBio-421350/2017-2//Instituto Chico Mendes de Conservação da Biodiversidade/ ; call no. 18/2017//National Council for Scientific and Technological Development/ ; },
abstract = {Evaluating microbial community changes in soils allows the understanding of ecoevolutionary dynamics, providing information on microbiome responses to anthropological interferences, reduced biodiversity, and climatic changes. The actinobacteria phylum plays crucial roles from an ecological point of view and is the focus of the present study, which tracked changes in the actinobacterial communities from Brazilian Cerrado soil in an environmental protection unit, based on different land uses. The evaluation of 16S rRNA and further taxonomical clustering of operational taxonomic units (OTUs) indicated Actinomycetales as the main order within all land uses, ranging from 45.4-70.1%, with Micrococales and Rubrobacterales being found only in agricultural soils. The evaluation of taxonomical classes revealed Actinobacteria as the main representative in all land uses (45.5-70.4%), with a paired coprevalence of Thermoleophilia (43.4%) in secondary soils, a taxon associated with phosphorus-deficient grounds. The unraveling of families and genera was most challenging due to the OTUs' dispersion given the volume of data, coupled with a high percentage of unidentified genera (71.6-86.1%), mainly in conserved and preserved areas. The reduced biodiversity, reduced undescribed taxa, and enhanced potentially pathogenic strains in anthropogenic affected sites, which suffer more from climatic changes, denote the harm that human activity causes to microbiological diversity.},
}

@article {pmid40282236,
year = {2025},
author = {Gamalero, E and Glick, BR},
title = {How Melatonin Affects Plant Growth and the Associated Microbiota.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040371},
pmid = {40282236},
issn = {2079-7737},
abstract = {Melatonin is found in all classes of living organisms. In particular, in plants melatonin acts as an antioxidant that helps plants deal with both biotic and abiotic stress. In plants, melatonin improves seed germination, fruit ripening, photosynthesis, biomass production, circadian rhythm, membrane integrity, root development, leaf senescence, osmoregulation, and stress modulation. Melatonin concentrations vary enormously in different plants, different plant growth stages, different plant organs, and both the season and time of day that a plant is harvested. In addition, melatonin promotes root growth and development, prevents leaf senescence, promotes flowering and fruit ripening, promotes lateral root formation, stimulates gene expression of enzymes involved in photosynthesis, and protects plants from phytopathogen attack. Moreover, melatonin produced by soil bacteria can affect plant tolerance and health; in turn, melatonin synthesized by plants can influence the soil and rhizosphere microbiome. Finally, very recent literature indicates that melatonin can directly and positively affect the functioning of other soil bacteria.},
}

@article {pmid40282197,
year = {2025},
author = {Chrustek, A and Dombrowska-Pali, A and Olszewska-Słonina, D and Wiktorczyk-Kapischke, N and Socha, MW and Budzyńska, A and Sadowska-Krawczenko, I},
title = {Human Milk Microbiome from Polish Women Giving Birth via Vaginal Delivery-Pilot Study.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040332},
pmid = {40282197},
issn = {2079-7737},
abstract = {UNLABELLED: The human milk (HM) microbiome is variable and depends on maternal, perinatal, and cultural-environmental factors. The diversity of the HM microbiome is crucial in the development of the child. The aim of the study was to assess the prevalence of bacteria (using culture-based methods) of Polish women with normal BMI, giving birth on time through vaginal delivery.

METHODS: The research material consisted of human milk and swabs from the areola and nipple, before and after breastfeeding, derived from Polish women (n = 86). Classic culture methods were used to obtain multiple bacteria. Species identification of the grown colonies was performed using MALDI TOF MS (Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry).

RESULTS: 120 species of bacteria were isolated, mainly from the genus Streptococcus and Staphylococcus. Species specific only to human milk were identified (belonging to the following genera: Microbacterium, Shewanella, Psychrobacter, Aeromonas, Serratia, Buttiauxella, Lactobacillus, Bifidobacterium) as well as species specific only to areola and nipple swabs after breastfeeding (Acinetobacter lactucae, Moraxella catarrhalis, Corynebacterium pseudodiphtheriticum, Corynebacterium propinquim). It was confirmed that most species were present in all tested materials collected from one patient.

CONCLUSIONS: The analysis carried out showed the presence of bacteria in the human milk of Polish women, including strains of lactic acid bacteria. The human milk microbiota may significantly influence the formation of the infant's intestinal microbiota, including some key genera, i.e., Lactobacillus, Bifidobacterium, and Limosilactobacillus, which were also isolated from the tested samples. The data presented here provide new data on culturable bacterial species isolated from breast milk from Polish women giving birth via vaginal delivery and potential routes of transmission from the neonate's oral cavity.},
}

@article {pmid40281983,
year = {2025},
author = {Hundam, S and Al-Zghoul, MB and Ababneh, M and Alanagreh, L and Dahadha, R and Mayyas, M and Alghizzawi, D and Mustafa, MA and Gerrard, DE and Dalloul, RA},
title = {Effects of Embryonic Thermal Manipulation on Body Performance and Cecum Microbiome in Broiler Chickens Following a Post-Hatch Lipopolysaccharide Challenge.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081149},
pmid = {40281983},
issn = {2076-2615},
support = {188/2019 and 400/2024//Deanship of Research at Jordan University of Science and Technology/ ; },
abstract = {Thermal manipulation (TM) during embryogenesis has emerged as a promising strategy to enhance post-hatch performance and improve resilience to environmental and bacterial stress, which offers a potential alternative to reduce the reliance on antibiotic growth promoters (AGPs) in broiler production. This study investigated TM's ability to modulate broilers' cecal microbiota and enhance resilience to lipopolysaccharide (LPS)-induced stress. Eggs in the control group (CON) were incubated at 37.8 °C and 56% relative humidity (RH), while TM eggs were exposed to 39 °C and 65% RH for 18 h daily from embryonic days 10-18. Post-hatch, the LPS subgroups (LPS-CON, LPS-TM) received intraperitoneal LPS injections, and body weight (BW) and temperature (BT) were monitored. Cecal samples were collected for microbiome sequencing. Alpha diversity showed no differences (p > 0.05), but beta diversity revealed differences between groups (PERMANOVA, p < 0.05). Firmicutes and Bacteroidota dominated the microbiota at the phylum level. Oscillospirales were enriched in the TM groups (p < 0.001) and Lactobacillales were increased in the LPS-CON group (p < 0.019). LPS reduced BT in the CON group (p < 0.01), but LPS-TM birds bypassed hypothermia. LPS significantly reduced BW (p < 0.001), while TM had no significant effect. These findings demonstrate TM's enduring influence on gut microbiota and stress resilience, highlighting its potential to reduce antibiotic reliance and mitigate antimicrobial resistance (AMR) in poultry production.},
}

@article {pmid40281970,
year = {2025},
author = {Khalid, N and Bukhari, SM and Ali, W and Sheikh, AA and Abdullah, HM and Nazmi, A},
title = {Probiotic Lactocaseibacillus casei NK1 Enhances Growth and Gut Microbiota in Avian Pathogenic Escherichia coli Challenged Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081136},
pmid = {40281970},
issn = {2076-2615},
abstract = {The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production.},
}

@article {pmid40281872,
year = {2025},
author = {Dipasquale, V and Romano, C},
title = {New Therapeutic Challenges in Pediatric Gastroenterology: A Narrative Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/healthcare13080923},
pmid = {40281872},
issn = {2227-9032},
abstract = {Pediatric gastroenterology is entering a pivotal phase marked by significant challenges and emerging opportunities in treating conditions like celiac disease (CeD), eosinophilic esophagitis (EoE), inflammatory bowel disease (IBD), and autoimmune hepatitis (AIH) pose significant clinical hurdles, but new therapeutic avenues are emerging. Advances in precision medicine, particularly proteomics, are reshaping care by tailoring treatments to individual patient characteristics. For CeD, therapies like gluten-degrading enzymes (latiglutenase, Kuma030) and zonulin inhibitors (larazotide acetate) show promise, though clinical outcomes are inconsistent. Immunotherapy and microbiota modulation, including probiotics and fecal microbiota transplantation (FMT), are also under exploration, with potential benefits in symptom management. Transglutaminase 2 inhibitors like ZED-1227 could help prevent gluten-induced damage. Monoclonal antibodies targeting immune pathways, such as AMG 714 and larazotide acetate, require further validation in pediatric populations. In EoE, biologics like dupilumab, cendakimab, dectrekumab (IL-13 inhibitors), and mepolizumab, reslizumab, and benralizumab (IL-5/IL-5R inhibitors) show varying efficacy, while thymic stromal lymphopoietin (TSLP) inhibitors like tezepelumab are also being investigated. These therapies require more pediatric-specific research to optimize their use. For IBD, biologics like vedolizumab, ustekinumab, and risankizumab, as well as small molecules like tofacitinib, etrasimod, and upadacitinib, are emerging treatments. New medications for individuals with refractory or steroid-dependent AIH have been explored. Personalized therapy, integrating precision medicine, therapeutic drug monitoring, and lifestyle changes, is increasingly guiding pediatric IBD management. This narrative review explores recent breakthroughs in treating CeD, EoE, IBD, and AIH, with a focus on pediatric studies when available, and discusses the growing role of proteomics in advancing personalized gastroenterological care.},
}

@article {pmid40281799,
year = {2025},
author = {Dubois, N and Giroux, I},
title = {Bidirectional Relationship Between Nutrition and Mental Health and Its Impact on the Health of Canadian Immigrants: An Integrative Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/healthcare13080850},
pmid = {40281799},
issn = {2227-9032},
abstract = {Background: Immigration is a key factor contributing to population growth in Canada, a trend that is expected to continue. Immigrants generally arrive with better health than the Canadian-born population, but this advantage often diminishes over time, partially due to dietary acculturation. Emerging evidence points to a bidirectional link between nutrition and mental health. Objective: To explore the bidirectional relationship between nutrition and mental health and its impact on the health of Canadian immigrants, with a specific focus on immigrants' mental health and the healthy immigrant effect. Methods: For this integrative review, two comprehensive literature searches were conducted in the databases MEDLINE, CINAHL, Embase, PsycINFO, Scopus, and Web of Science from inception to July 2024. The review adhered to Whittemore and Knafl's integrative methodology, with the Mixed Methods Assessment Tool used to assess the quality of the studies. Results: A total of 42 and 34 scientific articles were included from the first and second literature searches, respectively. Four main themes emerged from the literature: (1) food insecurity and mental health, (2) obesity and mental health, (3) diet quality and mental health, and (4) the gut microbiome and mental health. These themes were explored in the context of Canadian immigrants' health. Conclusions: The health of immigrants to Canada is likely shaped by complex, bidirectional interactions among various determinants of health, influencing both physical and mental well-being. As newcomers are expected to form an increasing proportion of the Canadian population, further research is needed to understand how the interaction between nutrition and mental health can help promote and safeguard the health of Canadian immigrants.},
}

@article {pmid40281786,
year = {2025},
author = {Yan, Y and Wang, Y and Tang, J and Liu, X and Wang, J and Song, G and Li, H},
title = {Comprehensive Analysis of Oncogenic Somatic Alterations of Mismatch Repair Gene in Breast Cancer Patients.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/bioengineering12040426},
pmid = {40281786},
issn = {2306-5354},
support = {QNJJ2022024//Clinical Research Fund for Distinguished Young Scholars of Peking University Cancer Hospital/ ; NNF22OC0080100//Novo Nordisk Fonden/ ; S23JRAR045//Agence Nationale de Recherche France/ ; },
abstract = {Recent clinical trials have suggested that solid cancers with mismatch repair (MMR) deficiency are highly responsive to immunotherapy, regardless of cancer types. Previous MMR-related studies on breast cancer have predominantly focused on germline variants. However, the somatic MMR alterations have not been comprehensively characterized in breast cancer. In this study, we integrated genomic, transcriptomic, and clinical data from over 3000 breast cancer cases across six public cohorts. Our findings revealed that 1.2% of breast cancers harbored oncogenic somatic MMR alterations, with triple-negative breast cancer (TNBC) demonstrating the highest mutation rate at 3.1%. Additionally, somatic MMR alterations were significantly associated with microsatellite instability-high (MSI-H) and MMR-related mutational signatures, indicating that somatic MMR alterations led to impaired function of the MMR system. Biallelic inactivation of MMR genes resulted in a more pronounced loss of MMR function compared to monoallelic inactivation. Importantly, these MMR alterations significantly increased the tumor mutational burden (TMB) and neoantigen load in breast cancer, regardless of MSI-H status. These findings indicate that the frequency of MMR alterations is highest in TNBC and that MMR alterations in breast cancer can lead to MMR functional deficiencies, suggesting that some patients harboring such alterations may benefit from immunotherapy.},
}

@article {pmid40281571,
year = {2025},
author = {Cai, Y and Fan, Y and Chen, A and Wang, X and Wang, L and Chen, J and Wang, Z and Li, J and Yi, X and Ju, C},
title = {Characteristics of upper and lower respiratory tract microbiota after lung transplantation.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {160},
pmid = {40281571},
issn = {1465-993X},
support = {ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2019GIRHZ04//Foundation from Guangzhou Institute of Respiratory Health/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Lung Transplantation/trends/adverse effects ; Prospective Studies ; Female ; Male ; *Microbiota/physiology ; Longitudinal Studies ; Middle Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Sputum/microbiology ; *Lung/microbiology ; Aged ; },
abstract = {BACKGROUND: The composition and characteristics of airway microbiota offer critical insights for clinical decision-making. Current research on chronic lung diseases shows differences in the composition and characteristics of upper and lower respiratory tract microbiota compared with healthy individuals. However, the temporal changes of these microbial communities in lung transplant recipients remain poorly characterized.

METHODS: This is a longitudinal prospective study. Respiratory specimens were collected regularly from lung transplant recipients for testing and analysis. A total of 150 bronchoalveolar lavage fluid (BALF) samples, 150 throat swab samples, 51 sputum samples, and 36 lung tissue samples were collected from the recipients, at 7 days, 14 days, 1 month, 2 months, 3 months, and 6 months post-transplant for 16S rRNA gene sequencing and analysis.

RESULTS: Our study showed that there were significant differences in α-diversity and β-diversity among lung tissue, throat swab, and sputum samples, although α-diversity did not show a significant difference between lung tissue and BALF. Most amplicon sequence variants (ASVs) belonged to the families Enterobacteriaceae, Pseudomonadaceae, and Stenotrophomonas in BALF, while most ASVs belonged to the genera Streptococcus, Pseudomonadaceae, and Stenotrophomonas in sputum samples. Regarding dynamic changes, Corynebacterium and Staphylococcus were more prevalent in the early post-operative period but gradually decreased by 7 days post-operatively, while the common microbiota found in healthy populations based on literature became the most abundant ASVs at 6 months post-operatively in our study participants. Pseudomonadaceae and Stenotrophomonas contributed to the similarity in the composition of upper and lower respiratory microbiota.

CONCLUSIONS: This study demonstrates that lung transplant recipients exhibit unique characteristics in their upper and lower respiratory tract microbiota, which are distinct ecological profiles, and both undergo significant changes within 6 months post-operatively. The similarity between upper and lower respiratory tract microbiota is associated with microbial diversity and taxonomic dominance.

CLINICAL TRIAL: The clinical trial was registered at Chinese Clinical Trial Registry (ChiCTR2200056908) in February 2022.},
}

Humans
*Lung Transplantation/trends/adverse effects
Prospective Studies
Female
Male
*Microbiota/physiology
Longitudinal Studies
Middle Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Sputum/microbiology
*Lung/microbiology
Aged

@article {pmid40281554,
year = {2025},
author = {Imani, S and Farghadani, R and Roozitalab, G and Maghsoudloo, M and Emadi, M and Moradi, A and Abedi, B and Jabbarzadeh Kaboli, P},
title = {Reprogramming the breast tumor immune microenvironment: cold-to-hot transition for enhanced immunotherapy.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {44},
number = {1},
pages = {131},
pmid = {40281554},
issn = {1756-9966},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Breast Neoplasms/immunology/therapy/pathology ; Female ; *Immunotherapy/methods ; Animals ; },
abstract = {This review discusses reprogramming the breast tumor immune microenvironment from an immunosuppressive cold state to an immunologically active hot state. A complex interplay is revealed, in which the accumulation of metabolic byproducts-such as lactate, reactive oxygen species (ROS), and ammonia-is shown to impair T-cell function and promote tumor immune escape. It is demonstrated that the tumor microenvironment (TME) is dominated by immunosuppressive cytokines, including interleukin-10 (IL-10), transforming growth factorβ (TGFβ), and IL-35. Notably, IL-35 is produced by regulatory T cells and breast cancer cells. The conversion of conventional T cells into IL-35-producing induced regulatory T cells, along with the inhibition of pro-inflammatory cytokine secretion, contributes to the suppression of anti-tumor immunity. It is further demonstrated that key immune checkpoint molecules-such as PD-1, PDL1, CTLA-4, TIM-3, LAG-3, and TIGIT-are upregulated within the TME, leading to Tcell exhaustion and diminished immune responses. The blockade of these checkpoints is shown to restore T-cell functionality and is proposed as a strategy to convert cold tumors into hot ones with robust effector cell infiltration. The therapeutic potential of chimeric antigen receptor (CAR)T cell therapy is also explored, and targeting specific tumor-associated antigens, such as glycoproteins and receptor tyrosine kinases, is highlighted. It is suggested that CART cell efficacy can be enhanced by combining these cells with immune checkpoint inhibitors and other immunomodulatory agents, thereby overcoming the barriers imposed by the immunosuppressive TME. Moreover, the role of the microbiome in regulating estrogen metabolism and systemic inflammation is reviewed. Alterations in the gut microbiota are shown to affect the TME, and microbiome-based interventions are proposed as an additional means to facilitate the cold-to-hot transition. It is concluded that by targeting the metabolic and immunological pathways that underpin immune suppression-through combination strategies involving checkpoint blockade, CART cell therapies, and microbiome modulation-the conversion of the breast TME from cold to hot can be achieved. This reprogramming is anticipated to enhance immune cell infiltration and function, thereby improving the overall efficacy of immunotherapies and leading to better clinical outcomes for breast cancer patients.},
}

Humans
*Tumor Microenvironment/immunology
*Breast Neoplasms/immunology/therapy/pathology
Female
*Immunotherapy/methods
Animals

@article {pmid40281400,
year = {2025},
author = {Binci, F and Cortese, E and Nouri, E and Capparotto, A and Guarneri, G and Settimi, AG and Dabalà, M and Antoni, V and Squartini, A and Giovannetti, M and Navazio, L},
title = {Plasma-activated water promotes and finely tunes arbuscular mycorrhizal symbiosis in Lotus japonicus.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {544},
pmid = {40281400},
issn = {1471-2229},
mesh = {*Mycorrhizae/physiology/drug effects ; *Lotus/microbiology/physiology/drug effects/metabolism ; *Symbiosis/drug effects ; *Water/pharmacology ; Plant Roots/microbiology ; *Plasma Gases/pharmacology ; },
abstract = {BACKGROUND: Plasma-activated water (PAW) is a recently developed cutting-edge technology that is increasingly gaining interest for its applications in medicine, food industry and agriculture. In plant biology, PAW has been shown to enhance seed germination, plant growth, and plant resilience against biotic and abiotic stresses. Despite increasing knowledge of the beneficial effects exerted by PAW on plants, little information is currently available about how this emerging technology may affect mutualistic plant-microbe interactions in the rhizosphere.

RESULTS: In this work we investigated the impact of irrigation with PAW, generated by a plasma torch, on arbuscular mycorrhizal (AM) symbiosis. Roots of the model legume Lotus japonicus expressing the bioluminescent Ca[2+] reporter aequorin responded to treatment with PAW 5' (obtained by 5 min water exposure to plasma) with the immediate induction of cytosolic and nuclear Ca[2+] signals, indicating that Ca[2+]-mediated signalling is one of the earliest cellular responses to PAW. The long-lasting elevations in intracellular Ca[2+] levels were not found to alter cell viability. Quantitative analyses of AM fungal accommodation in the host plant roots along with phosphate accumulation in leaves, as well as chemical analysis of N, C, S in shoots, showed that treatments with PAW play a modulatory role on plant AM symbiotic performance, in a manner dependent on the time interval of water exposure to the plasma and on the duration of plant treatment with PAW. In particular, irrigation with PAW 5' increased fungal colonization after 4 weeks, leading to a significant increase in leaf phosphate content after 7 weeks.

CONCLUSIONS: Our findings reveal that PAW enhances AM symbiosis by facilitating early fungal accommodation in roots and subsequently increasing phosphate content in leaves at later stages. A better understanding of the mechanisms underlying the effects of PAW on the plant microbiome may drive research towards a fine-tuning of this novel green technology to maximize its beneficial effects in the context of a more sustainable agriculture.},
}

*Mycorrhizae/physiology/drug effects
*Lotus/microbiology/physiology/drug effects/metabolism
*Symbiosis/drug effects
*Water/pharmacology
Plant Roots/microbiology
*Plasma Gases/pharmacology

@article {pmid40281290,
year = {2025},
author = {Basilio, H},
title = {Baffling chronic pain eases after doses of gut microbes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40281290},
issn = {1476-4687},
}

@article {pmid40281021,
year = {2025},
author = {Wu, Y and Tang, W and Ding, Y and Zhao, Y and Zhou, C and Cheng, Y and Dong, R and Li, Y and Zhao, G and Xu, A and Liu, Y},
title = {Enterococcus faecalis SI-FC-01 enhances the stress resistance and healthspan of C. elegans via AKT signaling pathway.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14454},
pmid = {40281021},
issn = {2045-2322},
support = {2023YFC3708303//National Key Research and Development Program of China/ ; 2308085UM08//Anhui Natural Science Advanced Functional Film Material Joint Foundation/ ; 2023t07020004//Anhui Provincial Key R&D Programs/ ; },
mesh = {*Caenorhabditis elegans/physiology/microbiology/metabolism ; Animals ; *Enterococcus faecalis/physiology ; *Proto-Oncogene Proteins c-akt/metabolism ; Caenorhabditis elegans Proteins/metabolism/genetics ; *Signal Transduction ; Longevity ; *Probiotics/pharmacology ; Oxidative Stress ; Forkhead Transcription Factors/metabolism ; *Stress, Physiological ; Aging ; Humans ; },
abstract = {The global demographic is witnessing an unprecedented surge in aging, precipitating a dramatic rise in geriatric diseases and related health complications. Although probiotics have been extensively shown to maintain microbiome stability and confer health benefits, their potential role in decelerating the aging process remains largely unexplored. The study identified a beneficial gut microbe from human intestinal tract, Enterococcus faecalis SI-FC-01, which was proved to be biosafe and found to enhance the average lifespan of C. elegans by 33.55%. More interestingly, the E. faecalis SI-FC-01 also enhanced the motor ability, memory and learning ability and anti-oxidative stress ability of C. elegans. Moreover, it exhibited neuroprotective effects in the worm models of neurodegenerative diseases such as Parkinson's disease and Huntington's disease. Through screening various aging-associated mutants of C. elegans, we discovered that E. faecalis SI-FC-01 modulates DAF-16/FOXO signaling via the activation of AKT pathway. This activation subsequently triggers stress resistance and immune-related genes downstream of daf-16, thereby promoting healthspan and neuroprotection. In summary, our research indicates that E. faecalis SI-FC-01 holds significant potential as a dietary supplement for delaying host aging. Furthermore, it provides novel insights for potentially mitigating the progression of age-related neurodegenerative diseases.},
}

*Caenorhabditis elegans/physiology/microbiology/metabolism
Animals
*Enterococcus faecalis/physiology
*Proto-Oncogene Proteins c-akt/metabolism
Caenorhabditis elegans Proteins/metabolism/genetics
*Signal Transduction
Longevity
*Probiotics/pharmacology
Oxidative Stress
Forkhead Transcription Factors/metabolism
*Stress, Physiological
Aging
Humans

@article {pmid40280980,
year = {2025},
author = {Beverly, ML and Chaudhary, PP and Dabdoub, SM and Kim, S and Chatzakis, E and Williamson, K and Ganesan, SM and Yadav, M and Ratley, G and D'Souza, BN and Myles, IA and Kumar, PS},
title = {Toxic cultures: e-cigarettes and the oral microbial exposome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {66},
pmid = {40280980},
issn = {2055-5008},
support = {DE027857//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; DE032895//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; },
mesh = {Humans ; *Biofilms/growth & development/drug effects ; *Electronic Nicotine Delivery Systems ; Saliva/microbiology/chemistry ; *Microbiota/drug effects ; *Mouth/microbiology ; *Bacteria/metabolism/genetics/drug effects/classification/isolation & purification ; Metabolomics ; Aerosols ; Quorum Sensing ; Vaping ; },
abstract = {We tested the hypothesis that e-cigarette aerosol is metabolized by the indigenous oral microbiome, leading to structural and functional alterations. We combined untargeted metabolomics of in vitro commensal-rich and pathogen-rich biofilms with metatranscriptomics and fluorescent microscopy and verified the results in human samples. Spectral deconvolution of 4215 peaks identified 969 exposomal and endogenous metabolites that mapped to 23 metabolic pathways. The metabolites clustered by both aerosol characteristics and biofilm composition; and several were verified in human saliva of vapers. E-cigarette exposure upregulated xenobiotic degradation, capsule, peptidoglycan biosynthesis, organic carbon-compound metabolism, antimicrobial resistance, and secretion systems. E-cigarette exposure also altered biofilm architecture characterized by low surface-area to biovolume ratio, high biomass, and diffusion distance. In conclusion, our data suggest that bacterial metabolism of e-cigarette aerosol triggers a quorum-sensing-regulated stress response which mediates the formation of dense, exopolysaccharide-rich biofilms in health-compatible communities and antibiotic resistance and virulence amplification in disease-associated communities.},
}

Humans
*Biofilms/growth & development/drug effects
*Electronic Nicotine Delivery Systems
Saliva/microbiology/chemistry
*Microbiota/drug effects
*Mouth/microbiology
*Bacteria/metabolism/genetics/drug effects/classification/isolation & purification
Metabolomics
Aerosols
Quorum Sensing
Vaping

@article {pmid40280962,
year = {2025},
author = {Wissel, EF and Chien, HY and Wei, KH and Lee, YC and Ullah, K and Hsieh, PCH},
title = {Microbial metabolites associated in stool and left ventricle of heart failure patients revealed by meta-analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14576},
pmid = {40280962},
issn = {2045-2322},
support = {110-2320-B-001-023-MY3//National Science and Technology Council/ ; 110-2320-B-001-023-MY3//National Science and Technology Council/ ; 110-2320-B-001-023-MY3//National Science and Technology Council/ ; 110-2320-B-001-023-MY3//National Science and Technology Council/ ; 110-2320-B-001-023-MY3//National Science and Technology Council/ ; 110-2320-B-001-023-MY3//National Science and Technology Council/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; NHRI-EX113-11203SI//National Health Research Institutes/ ; },
mesh = {Humans ; *Heart Failure/microbiology/metabolism ; *Feces/microbiology ; *Heart Ventricles/metabolism/microbiology ; Metabolomics/methods ; *Gastrointestinal Microbiome ; Metabolome ; },
abstract = {Heart Failure (HF) impacts approximately 64 million people globally. While overall incidence of HF is relatively stable across countries, the overall number of HF patients is increasing due to aging populations. Many articles examine the microbiome in HF, however, studies from humans have not been analyzed systematically. The aim of this meta-analysis is to bridge this gap by analyzing previously published data on human HF patients with untargeted metabolomics to understand whether microbially-mediated metabolites are consistently important for HF status. A systematic survey of the literature identified 708 articles discussing HF, the microbiome, and metabolomics. Of these, 82 were primary studies of HF patients, 61 studied human adults, 23 included an untargeted metabolomics measure, and 3 studies had data that was usable and publicly accessible. These studies include a GCMS study from stool, NMR of saliva and exhaled breath condensate, and LCMS from left ventricle of HF patients undergoing transplantation and unused donor hearts. Significant differences were observed from PCA between HF and controls for stool and left ventricle, but not saliva or EBC samples. OPLS-DA was conducted for stool and ventricle samples, and further revealed significant group differences. Univariate testing with FDR correction revealed 8 significant microbially-relevant metabolites (p < 0.005 after correction), most notably asparagine from left ventricle and 2-methylbutyryl carnitine from stool. Though there is much discussion of the microbiome in health outcomes in HF, there is limited research from human populations. Some microbial co-metabolites from both stool and heart were significantly associated with HF.},
}

Humans
*Heart Failure/microbiology/metabolism
*Feces/microbiology
*Heart Ventricles/metabolism/microbiology
Metabolomics/methods
*Gastrointestinal Microbiome
Metabolome

@article {pmid40280934,
year = {2025},
author = {Larkin, AA and Brock, ML and Fagan, AJ and Moreno, AR and Gerace, SD and Lees, LE and Suarez, SA and Eloe-Fadrosh, EA and Martiny, AC},
title = {Climate-driven succession in marine microbiome biodiversity and biogeochemical function.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3926},
pmid = {40280934},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; OCE-2135035//National Science Foundation (NSF)/ ; NA19NES4320002//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; 80NSSC21K1654//National Aeronautics and Space Administration (NASA)/ ; T32AI141346//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Microbiota/genetics ; *Biodiversity ; *Climate Change ; *Seawater/microbiology/chemistry ; Seasons ; Ecosystem ; California ; El Nino-Southern Oscillation ; Biomass ; Oceans and Seas ; Prochlorococcus/genetics ; Carbon/metabolism ; Bacteria/genetics/classification ; },
abstract = {Seasonal and El Niño-Southern Oscillation (ENSO) warming result in similar ocean changes as predicted with climate change. Climate-driven environmental cycles have strong impacts on microbiome diversity, but impacts on microbiome function are poorly understood. Here we quantify changes in microbial genomic diversity and functioning over 11 years covering seasonal and ENSO cycles at a coastal site in the southern California Current. We observe seasonal oscillations between large-genome lineages during cold, nutrient rich conditions in winter and spring versus small-genome lineages, including Prochlorococcus and Pelagibacter, in summer and fall. Parallel interannual changes separate communities depending on ENSO condition. Biodiversity shifts translate into clear oscillations in microbiome functional potential. Ocean warming induced an ecosystem with less iron but more macronutrient stress genes, depressed organic carbon degradation potential and biomass, and elevated carbon-to-nutrient biomass ratios. The consistent microbial response observed across time-scales points towards large climate-driven changes in marine ecosystems and biogeochemical cycles.},
}

*Microbiota/genetics
*Biodiversity
*Climate Change
*Seawater/microbiology/chemistry
Seasons
Ecosystem
California
El Nino-Southern Oscillation
Biomass
Oceans and Seas
Prochlorococcus/genetics
Carbon/metabolism
Bacteria/genetics/classification

@article {pmid40280882,
year = {2025},
author = {Sudermann, MA and Foster, ZSL and Dawson, SCL and Phan, H and Fieland, VJ and Martin, FN and Chang, JH and Grünwald, NJ},
title = {Demulticoder: An R Package for the Simultaneous Analysis of Multiplexed Metabarcodes.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0043-FI},
pmid = {40280882},
issn = {0031-949X},
abstract = {Metabarcoding is a widely used approach relying on short DNA sequences to identify organisms present in a community. While established workflows exist for analysis of single metabarcodes, these are cumbersome when multiple metabarcodes are required to study diverse taxa, such as those in plant- and soil-associated microbial communities, or when analyzing newly developed metabarcodes. To address this, we developed demulticoder, an R package automating the use of DADA2 to analyze data derived from multiple metabarcodes. It has novel capabilities that streamline data analysis by reducing the number of manual input steps and enabling automated processing of multiplexed metabarcodes. Additionally, demulticoder modularizes data processing to allow iterative quality control and reformats data for downstream analyses. We also updated the oomycete specific rps10 barcode database by revising the taxonomic information of select entries based on updates to the classifications within the NCBI Taxonomy database. A multiplex sequenced dataset consisting of ITS1 and rps10 metabarcodes from 162 samples and 12 controls was analyzed to compare demulticoder against a standard analysis workflow. Demulticoder required manual input at only four steps in comparison to 28 steps required for the standard workflow. Data quality and results from downstream exploratory, diversity, and differential abundance analyses were comparable to those from the standard workflow. Demulticoder is versatile and can be used to analyze datasets consisting of single metabarcodes, multiplexed and pooled metabarcode types, and different metabarcode types generated in separate experiments. The demulticoder R package, example datasets, and instructions are publicly accessible and open source.},
}

@article {pmid40280843,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Plant-microbe interactions: plants modulating their defenses.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.001},
pmid = {40280843},
issn = {1878-4372},
abstract = {Plant immunity is mediated by multiple factors, including microbial interactions and gene expression. Keppler et al. identified a set of microbe-responsive genes (general non-self response genes) whose expression or products affect bacterial strain abundance and enhance immunity. We explore how these genes shape alternative plant defense strategies for sustainable agriculture.},
}

@article {pmid40280799,
year = {2025},
author = {Price, L and Orgel, KA and Good, M},
title = {Donor human milk pasteurization methods and the effect on milk components as they relate to Necrotizing enterocolitis.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101638},
doi = {10.1016/j.siny.2025.101638},
pmid = {40280799},
issn = {1878-0946},
abstract = {Necrotizing enterocolitis (NEC) is an intestinal disease that predominantly occurs in preterm infants. While there are no definitive treatment options for NEC, the administration of human milk is protective against the development of NEC in preterm infants. However, human milk composition is highly dynamic, containing numerous bioactive components that can be affected by both maternal and perinatal factors. Furthermore, when maternal milk is unavailable, donor human milk, which goes through a rigorous preparation process including pooling and pasteurization, is used. The different pasteurization methods can have implications for the bioactive components of human milk. In this review, we explore the current literature surrounding the benefits of human milk in the prevention of NEC. We further review the bioactive components and the microbiome of human milk and the many factors that affect the diversity of milk content between human milk samples. Finally, we review the different methods of pasteurization and their effects on the components of human milk.},
}