@article {pmid40295327,
year = {2025},
author = {Thomson, P and Santibáñez, R and Garrido, D and Iturriaga, MP and Flores, C},
title = {Impact of Periodontal Disease on the Oral Microbiome of Cats.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {265},
pmid = {40295327},
issn = {1432-0991},
support = {Fondecyt Iniciación #11231174//ANID/ ; },
abstract = {Periodontal disease is a multifactorial condition commonly observed in domestic cats, characterized by inflammation and alveolar bone loss. This study aimed to elucidate the differences in the oral microbiome between healthy cats and those with periodontitis, focusing on microbial community structure and preliminary functionality. An observational case-control study was conducted involving 30 cats, divided equally into healthy and periodontitis groups. Gingival swabs were collected and analyzed using V3_V4 regions of the 16S rRNA sequencing. The results revealed that while the dominant phyla in both groups were Bacteroidota and Bacillota, cats with periodontitis exhibited decreased levels of Ochrobactrum, Odoribacter denticanis, Treponema denticola, Porphyromonas macacae, and Fretibacterium fastidiosum which are the characteristics of the periodontal oral microbiome. Predicted function indicated the enrichment of pathways related to the biosynthesis of fatty acids in periodontal disease, such as ubiquinol and mycolate production. These findings highlight significant microbial and functional shifts associated with feline periodontal disease, providing a basis for potential diagnostic and therapeutic strategies.},
}

@article {pmid40295236,
year = {2025},
author = {Ren, Q and Cui, C and Peng, Y and Zhou, Y and Zhang, H and Chen, L and Liu, Z},
title = {Causal relationship between gut microbiota and metabolic syndrome: A bidirectional Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {17},
pages = {e42179},
doi = {10.1097/MD.0000000000042179},
pmid = {40295236},
issn = {1536-5964},
abstract = {Metabolic syndromes (MetS) are complex metabolic disorders, the pathogenesis of which has not been fully elucidated. In recent years, the association between the gut microbiota and MetS has attracted widespread attention, but the causal relationship remains unclear. We performed a 2-sample Mendelian randomization analysis (MR) to examine whether the gut microbiota is causally related to MetS and its components to find a basis for potential diagnostic or intervention approaches for MetS. We utilized summary statistics from whole-genome association analyses of gut microbiota from the MiBioGen consortium and obtained MetS-related data from the UK Biobank, IEU Open GWAS project, and The Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC). MR analyses were performed using inverse variance weighted, MR-Egger, and weighted median. Sensitivity analyses were conducted to verify the robustness of the results. Among the 211 gut microbiota, we identified 8 that were significantly associated with the risk of MetS. Specifically, Lachnospiraceae (family), Veillonellaceae (family), Victivallaceae (family), Odoribacter (genus), and Olsenella (genus) may increase the risk of MetS, while Bifidobacteriaceae (family), Ruminococcaceae UCG-010 (genus), Actinobacteria (phylum) may decrease the risk of MetS. Additionally, we discovered that multiple microbiota are associated with various components of MetS, such as BMI, hypertension, and blood lipid levels. This study is the first to use MR methods to reveal the potential causal relationship between specific gut microbiota and MetS, providing a new perspective for understanding the pathogenesis of MetS, and offering important evidence for the development of gut microbiota-based prevention and treatment strategies for MetS.},
}

@article {pmid40295217,
year = {2025},
author = {Nguyen, TT and Kim, YK and Ko, D and Kim, J and Yi, H and Bang, YJ},
title = {Development of the First Shuttle Vector System and Optimization of Transformation in Selenomonas sputigena.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2501011},
doi = {10.4014/jmb.2501.01011},
pmid = {40295217},
issn = {1738-8872},
abstract = {Selenomonas sputigena, an anaerobic bacterium found in the human respiratory tract, has recently gained significant attention due to its dual role in human health - as both a periodontal pathogen and a protective agent against severe asthma. However, the absence of genetic tools for this organism has severely limited our understanding of its molecular mechanisms and therapeutic potential. Here, we report the first successful development of a genetic modification system for S. sputigena ATCC 35185. We constructed a shuttle vector carrying the Rep191 replication protein from Selenomonas ruminantium and systematically optimized transformation conditions. Through careful optimization of key parameters including DNA quantity, bacterial growth phase, membrane permeabilization, and post-pulse recovery time, we achieved a 22.5-fold improvement in transformation efficiency (from ~2,000 to ~45,000 CFU/μg DNA). The broad applicability of our system was demonstrated through successful transformation of multiple Selenomonas species, establishing the first standardized genetic modification system for this genus. We further validated the system's functionality by achieving stable GFP expression in S. sputigena, representing the first demonstration of ectopic protein expression in this organism. This work provides essential tools for investigating the molecular basis of S. sputigena's therapeutic effects and pathogenic capabilities, potentially accelerating the development of novel microbiome-based treatments for both respiratory and oral diseases.},
}

@article {pmid40295202,
year = {2025},
author = {Lee, SM and Kong, HG and Lee, B and Chang, YK and Ryu, CM},
title = {Management of Naturally Occurring Diseases by Supernatant from Chlorella Cultures in Pepper.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502004},
doi = {10.4014/jmb.2502.02004},
pmid = {40295202},
issn = {1738-8872},
abstract = {The large-scale culture of Chlorella, a genus of microalgae, generates valuable products used to improve human health and produce biofuel. Such commercial applications utilized only the microalgal cells. However, the process produces tons of supernatant waste that require detoxification and disposal. A previous study demonstrated that cell-free supernatants from Chlorella fusca culture primes plant immunity in the model plant Arabidopsis thaliana, suggesting its potential for use as a bioprotectant. The current study investigated the effects of treatment with Chlorella supernatant on crop plants in an agricultural setting. Supernatants from Chlorella sp. strains HS2 and ABC001 were drench-applied to pepper (Capsicum annum L.) seedlings under greenhouse and field conditions. The disease control capacity and growth of plants were evaluated, as well as the diversity of the rhizosphere microbiota. Application of either supernatant reduced the severity of bacterial leaf spot disease caused by Xanthomonas axonopodis pv. vesicatoria and enhanced pepper seedling growth in the greenhouse. Under field conditions, cell-free supernatants of strains HS2 and ABC001 not only reduced the severity of natural-occurring viral and bacterial diseases and insect infestation but also increased fruit yield. Additionally, drenching with Chlorella supernatants improved species diversity in the rhizosphere microbiota. The application of Chlorella supernatant to pepper therefore offered protection against diverse field pathogens and promoted seedling growth and productivity. Our finding provides insight into novel methods of sustainable agriculture utilizing recycled cell-free waste supernatants from the industrial culture of Chlorella.},
}

@article {pmid40295198,
year = {2025},
author = {Chaudhary, DK and Kim, SE and Park, HJ and Kim, KH},
title = {Microbacterium chionoecetis sp. nov. and Agrococcus chionoecetis sp. nov.: Novel Gut Bacteria from Red Snow Crab.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412044},
doi = {10.4014/jmb.2412.12044},
pmid = {40295198},
issn = {1738-8872},
abstract = {Two yellow-coloured, Gram-stain-positive, oxidase-negative, aerobic, non-motile, and rod-shaped strains, labelled as ProA8[T] and ProA11[T], were isolated from digestive tract of red snow crab (Chionoecetes japonicus). Strain ProA8[T] grow at temperature range of 15-35°C, while strain ProA11[T] grow at temperature range of 15-40°C. Phylogenetic and 16S rRNA gene sequence analysis revealed that strains ProA8[T] and ProA11[T] belonged to the genera Microbacterium and Agrococcus, respectively. Strain ProA8[T] was closely affiliated with Microbacterium yannicii JCM 18959[T] (98.8%) and strain ProA11[T] was most closely related to Agrococcus baldri IAM 15147[T] (98.9%). The genome sizes of ProA8[T] and ProA11[T] were 4,373,776 bp and 2,665,899 bp, with DNA G+C contents of 70.5% and 70.1%, respectively. The genomic relatedness values of ProA8[T] and ProA11[T] with their respective reference strains were <32.0% (for digital DNA-DNA hybridization) and <87.0% (for average nucleotide identity). Biosynthetic gene analysis showed the presence of genes for resorcinol production in ProA8[T] and ectoine biosynthesis in ProA11[T], indicating ecological and biotechnological significance. Virulence analyses determined that strains ProA8[T] and ProA11[T] were non-pathogenic to humans, highlighting their safe application in biotechnological field. The major cellular fatty acids reported in ProA8[T] and ProA11[T] were anteiso-C15:0, iso-C16:0, and anteiso-C17:0. Overall, the polyphasic taxonomic data suggest that both strains ProA8[T] and ProA11[T] represent two novel species within the genera Microbacterium and Agrococcus, respectively. Accordingly, we propose the names Microbacterium chionoecetis sp. nov., with the type strain ProA8[T] (= KCTC 49861[T] = JCM 37392[T]) and Agrococcus chionoecetis sp. nov., with the type strain ProA11[T] (= KCTC 49958[T] = JCM 37393[T]).},
}

@article {pmid40295195,
year = {2025},
author = {Ali, M and Iqbal, N and Rakib, MA and Lee, KA and Lee, MH and Kim, YS},
title = {Microbiome, Potential Therapeutic Agents: New Players of Obesity Treatment.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2501024},
doi = {10.4014/jmb.2501.01024},
pmid = {40295195},
issn = {1738-8872},
abstract = {Obesity is a global pandemic, and recent research has established a correlation between the microbiome and obesity, indicating potential treatment possibilities. This review evaluated the potential of the microbiome in treating obesity by targeting anti-adipogenesis and adipose tissue browning mechanisms. The microbiome impacts adipogenesis through lipogenesis and inflammation pathways and influences adipose tissue browning via the secretion of gut hormones and short-chain fatty acids. Understanding these mechanisms could pave the way for interventions targeting the gut microbiome to reduce obesity-related adiposity. While our understanding of the specific microbial species, metabolites, and signaling pathways involved in these processes is still limited, this review highlights the potential of microbiome-based therapies for obesity. Further research focused on identifying key microbial players and their mechanisms of action will be crucial for developing targeted and effective interventions. This will ultimately contribute to a more comprehensive understanding of obesity pathogenesis and facilitate the development of novel therapeutic strategies to combat this global health crisis.},
}

@article {pmid40295129,
year = {2025},
author = {Roy Paladhi, U and Workneh, F and Baye, E and Derebe, MM and Yibeltal, K and Fasil, N and Driker, S and Van Dyk, F and I Chin, T and North, K and Jensen, SKG and Christian, P and Worku, A and Berhane, Y and Lee, AC},
title = {Investigating biological mechanisms of adverse birth outcomes and early child development in Amhara, Ethiopia: protocol of biospecimen collection and analysis of the Enhancing Nutrition and Antenatal Infection Treatment (ENAT) randomised effectiveness study.},
journal = {BMJ open},
volume = {15},
number = {4},
pages = {e098686},
doi = {10.1136/bmjopen-2024-098686},
pmid = {40295129},
issn = {2044-6055},
abstract = {INTRODUCTION: Maternal undernutrition and infections during pregnancy may influence birth and long-term child development outcomes. Characterising the micronutrient, metabolomic and microbiome profiles of pregnant women and infants may elucidate the underlying biology of adverse birth outcomes and early child development in the first 1000 days.

METHODS AND ANALYSIS: The Enhancing Nutrition and Antenatal Infection Treatment (ENAT) study was a 2×2 factorial, randomised clinical effectiveness study conducted in Amhara, Ethiopia from August 2020 to June 2022. We cluster-randomised pregnant women (n=2399) to receive either a nutrition intervention (iron-folic acid (IFA), iodised salt and balanced energy-protein supplementation for women with mid-upper arm circumference <23 cm) or routine care (IFA only), and individually randomised women to an infection control intervention (genitourinary tract infection screening-treatment and screening-treatment of stool parasites) or routine care (syndromic approach). Participants were followed until 1 month postpartum. A subset of 532 women-infant dyads were consecutively enrolled in the biospecimen substudy from July 2021 to August 2022. Specimens were collected at enrolment (<24 weeks) and antenatal care follow-up (third trimester), and 1-6 months postdelivery. A subset of ENAT mother-infant dyads (n=462) was enrolled in the Longitudinal Infant Development and Growth study that followed infants until 24 months postpartum, from February 2023 to June 2024. We will determine the impact of ENAT interventions on micronutrient status, inflammation biomarkers and metabolomic and microbiome profiles. We will also determine the association of these profiles with birth outcomes and infant neurodevelopment.

ETHICS AND DISSEMINATION: These studies were approved by the Institutional Review Boards of Addis Continental Institute of Public Health (ACIPH/IRB/002/2022) and Mass General Brigham (2023P000461). Results will be disseminated to international stakeholders via peer-reviewed journals and locally via strategic dissemination sessions.

TRIAL REGISTRATION NUMBERS: ISRCTN15116516 and NCT06296238.},
}

@article {pmid40295121,
year = {2025},
author = {Scheffer, G and Rattray, J and Evans, P and Shi, W and Bhatnagar, S and Hubert, CRJ},
title = {Nitrate-reducing microorganisms prevent souring of an oil field produced water storage pond.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf041},
pmid = {40295121},
issn = {1574-6941},
abstract = {Nitrate addition for mitigating sulfide production in oilfield systems has been studied in laboratory settings and in some subsurface oil reservoirs. To promote water recycling and re-use associated with oil reservoirs produced by hydraulic fracturing, high-salinity produced waters are temporarily stored in surface ponds prior to subsequent reinjection into the subsurface. In this study, nitrate was added directly to a storage pond to prevent sulfide accumulation. DNA sequencing of pond water over a 4-week period revealed a decrease in the proportion of sulfate-reducing microorganisms following nitrate application. Sulfate levels remained stable during this period, whereas nitrate and nitrite fluctuated in the days following the nitrate addition. Metagenome-assembled genomes (MAGs) reconstructed from the pond water microbiome highlighted different organisms with genes for organoheterotrophic and lithoheterotrophic nitrate reduction, whereas genes associated with sulfide production via sulfate or thiosulfate reduction were barely detected. Within those MAGs, genes for acetate metabolism were observed, consistent with acetate decreasing substantially in the pond water in the presence of nitrate. After nitrate was consumed an increase in relative abundance of putative autotrophic microorganisms was observed (e.g. Arhodomonas, Guyparkeria, Psychroflexus), corresponding to a drop in total inorganic carbon measurements in the storage pond. This trial offers an overview on microbial processes taking place in storage pond environments in response to nitrate addition.},
}

@article {pmid40295093,
year = {2025},
author = {Shi, X and Zhu, F and Min, W},
title = {VTrans: A VAE-Based Pre-Trained Transformer Method for Microbiome Data Analysis.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/cmb.2024.0884},
pmid = {40295093},
issn = {1557-8666},
abstract = {Predicting the survival outcomes and assessing the risk of patients play a pivotal role in comprehending the microbial composition across various stages of cancer. With the ongoing advancements in deep learning, it has been substantiated that deep learning holds the potential to analyze patient survival risks based on microbial data. However, confronting a common challenge in individual cancer datasets involves the limited sample size and the high dimensionality of the feature space. This predicament often leads to overfitting issues in deep learning models, hindering their ability to effectively extract profound data representations and resulting in suboptimal model performance. To overcome these challenges, we advocate the utilization of pretraining and fine-tuning strategies, which have proven effective in addressing the constraint of having a smaller sample size in individual cancer datasets. In this study, we propose a deep learning model that amalgamates Transformer encoder and variational autoencoder (VAE), VTrans, employing both pre-training and fine-tuning strategies to predict the survival risk of cancer patients using microbial data. Furthermore, we highlight the potential of extending VTrans to integrate microbial multi-omics data. Our method is assessed on three distinct cancer datasets from The Cancer Genome Atlas Program, and the research findings demonstrated that (1) VTrans excels in terms of performance compared to conventional machine learning and other deep learning models. (2) The utilization of pretraning significantly enhances its performance. (3) In contrast to positional encoding, employing VAE encoding proves to be more effective in enriching data representation. (4) Using the idea of saliency map, it is possible to observe which microbes have a high contribution to the classification results. These results demonstrate the effectiveness of VTrans in prediting patient survival risk. Source code and all datasets used in this paper are available at https://github.com/wenwenmin/VTrans and https://doi.org/10.5281/zenodo.14166580.},
}

@article {pmid40294213,
year = {2025},
author = {Israr, MZ and Salzano, A and Zhan, H and Voors, AA and Ng, LL and Suzuki, T},
title = {Risk calculator of multimorbid risk of rehospitalisation and death from heart failure - including the contribution of the gut microbiome.},
journal = {European journal of preventive cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/eurjpc/zwaf270},
pmid = {40294213},
issn = {2047-4881},
abstract = {BACKGROUND: The elucidation of the contributory role of multimorbidity to heart failure (HF) including the gut-heart axis has added a new dimension to our understanding of HF pathophysiology which is not reflected in currently available risk scores. The present investigation aimed to develop and validate a novel risk score model of multimorbidity for HF risk stratification.

METHODS: A risk model was developed based on the contribution of markers associated with HF multimorbidities on outcomes of mortality and/or rehospitalization due to HF (death/HF) at one year. Two independent HF cohorts were combined and randomly split 70:30 using a split-sample validation approach for training and validation cohorts which were not significantly different for investigated variables. Backward logistic regression was used to develop the risk model with a further scoring system to create a simple risk calculator.

RESULTS: A final 11-variable risk model (age, previous HF hospitalization, NYHA group III/IV, NT-proBNP, diastolic blood pressure, loop diuretic use, beta-blocker non-use, creatinine, COPD, diabetes, and combined gut metabolites) showed a diagnostic performance of 0.71 in the training cohort (C-statistic validation cohort, 0.70, p<0.001). A risk score/calculator was further developed based on this model with categorization into three (low-, mid- and high-) and two (low- and high-) risk groups, with both approaches demonstrating increased incidence of death/HF in patients at the highest risk (p<0.001).

CONCLUSION: A novel risk model and score were derived which showed the contribution of comorbidities including the added value of the gut-heart axis on risk stratification of HF patients on rehospitalization and death.},
}

@article {pmid40293987,
year = {2025},
author = {Leps, AS and Packeiser, EM and Schwens, C and Stoelcker, B and Doric, S and Wirkner, M and Walter, B and Wehrend, A and Kichmann, V and Jung, K and Goericke-Pesch, S},
title = {The canine vaginal microbiome during heat and fertility in healthy breeding dogs.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0321683},
doi = {10.1371/journal.pone.0321683},
pmid = {40293987},
issn = {1932-6203},
mesh = {Animals ; Female ; Dogs ; *Vagina/microbiology ; *Fertility/physiology ; *Microbiota ; *Hot Temperature ; Pregnancy ; Breeding ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {A healthy and balanced vaginal microbiome is often thought to be an important prerequisite for successful breeding and healthy litters. Previous studies investigating the influence of canine vaginal bacteria on fertility mostly relied on aerobic culturing. In recent years, culture-independent methods, such as next-generation sequencing (NGS), have become popular. With the ability to analyze the microbiome as a whole, research in this field has made notable advances. This is the first study to correlate NGS data of the canine vaginal microbiome in heat with fertility data. Healthy breeding bitches (n=80) presented for routine pre-breeding examination were sampled during early heat and mated after ovulation. A vaginal sample was taken for NGS analysis and microbiological culture. Additionally, a blood sample was collected. Fertility data (mating, pregnancy, delivery, litter size) were assessed. NGS revealed a diverse microbiome in all the samples. Bioinformatics and statistical analysis did not provide evidence of larger differences in the microbiome of those bitches that became pregnant and those that did not.},
}

Animals
Female
Dogs
*Vagina/microbiology
*Fertility/physiology
*Microbiota
*Hot Temperature
Pregnancy
Breeding
High-Throughput Nucleotide Sequencing
Bacteria/genetics/classification/isolation & purification

@article {pmid40293426,
year = {2025},
author = {Mirhosseini, SM and Rezaei, M and Soltanipur, M and Yarmohammadi, H and Soroush, E and Taromiha, A and Ebrahimzadeh, N and Nour Neamatollahi, A and Fateh, A and Hatefi, F and Douroud, D and Panahi, J and Jafari Naeini, S and Siadat, SD},
title = {Gut microbiome composition and one-year survival outcomes among patients with reduced ejection fraction heart failure.},
journal = {Cardiology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000545877},
pmid = {40293426},
issn = {1421-9751},
abstract = {BACKGROUND: Imbalances in gut microbiota are linked to chronic diseases, including heart failure, where shifts in microbial composition are evident in patients with reduced ejection fraction (HFrEF). This study compared gut microbiome profiles between HFrEF patients and healthy controls and explored potential links between microbiome composition and patient survival over 6 and 12 months.

METHODS: In this longitudinal case-control study, 20 HFrEF patients and 40 healthy controls were recruited, with stool samples collected for gut microbiome analysis. Patients were followed for six and twelve months to assess survival. Gut microbiome composition was analyzed using real-time PCR for specific bacterial taxa. Statistical analyses were performed using R to compare HFrEF and control groups and draw the ROC curve to predict survival at six and twelve months.

RESULTS: HFrEF patients showed a significantly lower abundance of all bacterial taxa, except for A. muciniphila. Decreased levels of Prevotella, F. prausnitzii, Firmicutes, and Bacteroides, as well as a lower Firmicutes/Bacteroidetes (F/B) ratio, were notable in HFrEF patients, with specific taxa correlating with clinical features like ascites and vitamin D levels. Most bacterial taxa and the F/B ratio could distinguish HFrEF patients from controls, though none effectively predicted survival outcomes at six or twelve months.

CONCLUSION: The study demonstrates that patients with HFrEF exhibit a distinct gut microbiome profile compared to healthy individuals. While specific gut bacteria were effective in distinguishing HFrEF patients from healthy controls, their ability to predict survival outcomes was limited, highlighting the need for further research into the role of the gut microbiome in the progression and prognosis of heart failure.},
}

@article {pmid40293249,
year = {2025},
author = {Zhang, X and Guan, F and Gou, W and Wang, Q and Du, S and Su, C and Zhang, J and Zheng, J-S and Wang, H and Zhang, B},
title = {Multi-trajectories of BMI, waist circumference, gut microbiota, and incident dyslipidemia: a 27-year prospective study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0024325},
doi = {10.1128/msystems.00243-25},
pmid = {40293249},
issn = {2379-5077},
abstract = {Evidence is insufficient to establish a longitudinal association between combined trajectories of body mass index (BMI) and waist circumference (WC) and dyslipidemia. This study investigated the associations between multi-trajectories of BMI and WC over 24 years and the subsequent risk of dyslipidemia in a large cohort of 10,678 Chinese adults from the China Health and Nutrition Survey. Utilizing a group-based trajectory model, we identified four distinct trajectories: normal, normal-increasing, overweight-increasing, and obesity-increasing. Our results indicated that ascending trajectories of BMI and WC are significantly associated with increased odds of dyslipidemia, particularly in males, with odds ratios (OR) of 2.10, 2.69, and 3.56 for the normal-increasing, overweight-increasing, and obesity-increasing groups, respectively. Among females, the normal-increasing group exhibited a significant increased risk (OR: 1.54). Furthermore, we explored the gut microbiota associated with these trajectories, identifying 3, 8, and 4 bacterial genera linked to increasing BMI and WC in males, alongside two genera in females with the normal-increasing trajectory. We identified a total of 23, 25, and 10 differential metabolites significantly associated with these genera, except for Group 2 in males. The inclusion of relevant microbiome and metabolite data improved the model's predictive capacity for the risk of dyslipidemia, with ROC values increasing from 0.655 to 0.875. Our findings underscore the critical implications of continuous weight gain on metabolic health and suggest that gut microbiota may play a pivotal role in understanding these associations.IMPORTANCEEmerging evidence suggests a close connection between the gut microbiome and both human obesity and dyslipidemia, suggesting that the gut microbiome may play an important role in the obesity-dyslipidemia relationship. In this study, we observed several characteristic genera, including Clostridium_sensu_stricto_1, Turicibacter, and CHKCI002 among males and Parabacteroides and [Eubacterium]_brachy_group among females, which were negatively associated with high-risk trajectories. They were also related to free fatty acids (FFAs) and oxidized lipid metabolites. These shared and unique gut microbial and metabolic signatures among combined trajectories of BMI and WC with a higher risk of dyslipidemia could provide important evidence for the omics mechanism pathway of long-term obesity trend leading to dyslipidemia.},
}

@article {pmid40293161,
year = {2025},
author = {de Córdoba-Ansón, PF and Linares-Ambohades, I and Baquero, F and Coque, TM and Pérez-Cobas, AE},
title = {The Respiratory Tract Microbiome and Human Health.},
journal = {Microbial biotechnology},
volume = {18},
number = {5},
pages = {e70147},
doi = {10.1111/1751-7915.70147},
pmid = {40293161},
issn = {1751-7915},
support = {2023-T1/SAL-GL28953//Comunidad de Madrid/ ; PEJ-2024-AI/SAL-GL-31755//Comunidad de Madrid/ ; PI23/01036//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Microbiota ; *Respiratory System/microbiology ; *Respiratory Tract Diseases/microbiology/therapy ; Dysbiosis ; },
abstract = {The respiratory tract microbiome (RTM) is a multi-kingdom microbial ecosystem that inhabits various niches of the respiratory system. While previously overlooked, there is now sufficient evidence that the RTM plays a crucial role in human health related to immune system training and protection against pathogens. Accordingly, dysbiosis or disequilibrium of the RTM has been linked to several communicable and non-communicable respiratory diseases, highlighting the need to unveil its role in health and disease. Here, we define the RTM and its place in microbiome medicine. Moreover, we outline the challenges of RTM research, emphasising the need for combining methodologies, including multi-omics and computational tools. We also discuss the RTM's potential for diagnosing, preventing and treating respiratory diseases and developing novel microbiome-based therapies to improve pulmonary health.},
}

Humans
*Microbiota
*Respiratory System/microbiology
*Respiratory Tract Diseases/microbiology/therapy
Dysbiosis

@article {pmid40292517,
year = {2025},
author = {Mallardi, D and Maqoud, F and Guido, D and Aloisio, M and Linsalata, M and Russo, F},
title = {Mapping Research Trends on Intestinal Permeability in Irritable Bowel Syndrome with a Focus on Nutrition: A Bibliometric Analysis.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17061064},
pmid = {40292517},
issn = {2072-6643},
support = {RC 2024//Italian Ministry of Health/ ; },
mesh = {*Irritable Bowel Syndrome/physiopathology/microbiology ; Humans ; *Bibliometrics ; Gastrointestinal Microbiome/physiology ; Permeability ; *Intestinal Mucosa/metabolism ; Diet ; *Biomedical Research/trends ; Intestinal Barrier Function ; },
abstract = {Irritable Bowel Syndrome (IBS) is a complex gastrointestinal disorder characterized by chronic abdominal pain and altered bowel habits, often linked to disruptions in intestinal barrier function. Increased intestinal permeability plays a key role in IBS pathogenesis, affecting immune responses, gut microbiota, and inflammation. This study conducts a bibliometric analysis to explore global research trends on intestinal permeability in IBS, focusing on key contributors, collaboration networks, and thematic shifts, particularly the interplay between the intestinal barrier, gut microbiota, and dietary components. A total of 411 articles were retrieved from Scopus, with 232 studies analyzed using Bibliometrix in R. To optimize screening, ASReview, a machine learning tool, was employed, utilizing the Naïve Bayes algorithm combined with Term Frequency-Inverse Document Frequency (TF-IDF) for adaptive ranking of articles by relevance. This approach significantly improved screening step efficacy. The analysis highlights growing research interest, with China and the USA as leading contributors. Key themes include the role of gut microbiota in modulating permeability, the impact of dietary components (fiber, probiotics, bioactive compounds) on tight junction integrity, and the exploration of therapeutic agents. Emerging studies suggest integrating gut barrier modulation with nutritional and microbiome-targeted strategies for IBS management. This study provides a comprehensive overview of research on intestinal permeability in IBS, mapping its evolution and identifying major trends. By highlighting key contributors and thematic areas, it offers insights to guide future investigations into the interplay between gut permeability, diet, and microbiota, advancing understanding of IBS pathophysiology and management.},
}

*Irritable Bowel Syndrome/physiopathology/microbiology
Humans
*Bibliometrics
Gastrointestinal Microbiome/physiology
Permeability
*Intestinal Mucosa/metabolism
Diet
*Biomedical Research/trends
Intestinal Barrier Function

@article {pmid40292481,
year = {2025},
author = {Abbasi, M and Heath, B and McGinness, L},
title = {Effects of Multivitamin Supplementation on Metabolic Parameters in High- and Low-Fat Diet-Fed C57BL/6J Mice: Potential Links to Adipose Tissue Browning and Gut Microbiome.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17061045},
pmid = {40292481},
issn = {2072-6643},
support = {ALA043-1-19235//National Institute of Food and Agriculture/ ; U24 DK132740/NH/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Diet, High-Fat/adverse effects ; Male ; *Dietary Supplements ; *Vitamins/pharmacology/administration & dosage ; *Adipose Tissue, Brown/metabolism/drug effects ; Mice ; Energy Metabolism/drug effects ; Adipose Tissue, White/metabolism/drug effects ; Obesity/metabolism ; *Diet, Fat-Restricted ; Thermogenesis/drug effects ; Insulin Resistance ; Blood Glucose/metabolism ; },
abstract = {BACKGROUND/OBJECTIVES: The relationship between diet, micronutrient supplementation, and metabolic regulation emphasizes the potential of nutritional strategies to address obesity and related disorders. Certain vitamins have the potential to enhance thermogenesis and metabolic health. However, the impact of multivitamin supplementation on white adipose tissue (WAT) browning, the gut microbiome (GM), and metabolic function is not well understood. This study investigated the effects of multivitamin supplementation on obesity-related metabolic dysfunction in mice fed a high-fat diet (HFD) or a low-fat diet (LFD).

METHODS: Male C57BL/6J mice were assigned to group 1: control chow diet (CHD); 2: control HFD; 3: multivitamin-supplemented HFD (Mv-HFD); 4: control LFD; or 5: multivitamin-supplemented LFD (Mv-LFD). Diets, either supplemented with multivitamins A, D, B1, B5, and C or non-supplemented, were administered for 12 weeks. Metabolic parameters, adipose tissue browning, and the GM composition were analyzed.

RESULTS: The Mv-HFD significantly reduced weight gain, adipose tissue mass, blood glucose levels, and insulin resistance induced by an HFD. Additionally, it increased energy expenditure and thermogenic gene expression in WAT. Both the Mv-HFD and Mv-LFD improved the GM composition by increasing beneficial bacteria.

CONCLUSIONS: Multivitamin supplementation improved metabolic health by potentially promoting WAT browning, enhancing energy expenditure, and modulating the GM composition. These findings suggest that multivitamins could offer a promising strategy for combating obesity and associated metabolic dysfunction.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Diet, High-Fat/adverse effects
Male
*Dietary Supplements
*Vitamins/pharmacology/administration & dosage
*Adipose Tissue, Brown/metabolism/drug effects
Mice
Energy Metabolism/drug effects
Adipose Tissue, White/metabolism/drug effects
Obesity/metabolism
*Diet, Fat-Restricted
Thermogenesis/drug effects
Insulin Resistance
Blood Glucose/metabolism

@article {pmid40292452,
year = {2025},
author = {Biagioli, V and Matera, M and Ramenghi, LA and Falsaperla, R and Striano, P},
title = {Microbiome and Pregnancy Dysbiosis: A Narrative Review on Offspring Health.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17061033},
pmid = {40292452},
issn = {2072-6643},
mesh = {Humans ; Pregnancy ; Female ; *Dysbiosis/microbiology/complications ; *Pregnancy Complications/microbiology ; Gastrointestinal Microbiome ; Fetal Development ; *Prenatal Exposure Delayed Effects ; *Microbiota ; Neurodevelopmental Disorders/microbiology ; Pregnancy Outcome ; Probiotics ; },
abstract = {Background: Emerging evidence suggests that the maternal microbiome plays a crucial role in shaping fetal neurodevelopment, immune programming, and metabolic health. Dysbiosis during pregnancy-whether gastrointestinal, oral, or vaginal-can significantly influence pregnancy outcomes and long-term child health. Materials and Methods: The search was performed using databases such as PubMed, Scopus, and Google Scholar including research published from January 2000 to January 2025. The keywords used were "Fetal Programming", " Maternal Immune Activation", "Maternal microbiome", "Microbiota-Gut-Brain Axis", and "Pregnancy Dysbiosis". Results: The maternal microbiome undergoes substantial changes during pregnancy, with alterations in microbial diversity and function linked to conditions such as gestational diabetes, obesity, and preeclampsia. Pregnancy-related dysbiosis has been associated with adverse neurodevelopmental outcomes, including an increased risk of autism spectrum disorder (ASD), attention-deficit/hyperactivity disorder (ADHD), and cognitive impairments in offspring. Conclusions: Understanding the intricate relationship between maternal microbiota and fetal health is essential for developing targeted interventions. Personalized microbiome-based strategies, including dietary modifications and probiotic supplementation, hold promise in optimizing pregnancy outcomes and promoting health in offspring.},
}

Humans
Pregnancy
Female
*Dysbiosis/microbiology/complications
*Pregnancy Complications/microbiology
Gastrointestinal Microbiome
Fetal Development
*Prenatal Exposure Delayed Effects
*Microbiota
Neurodevelopmental Disorders/microbiology
Pregnancy Outcome
Probiotics

@article {pmid40292334,
year = {2025},
author = {Comertpay, B and Gov, E},
title = {Multiomics Analysis and Machine Learning-based Identification of Molecular Signatures for Diagnostic Classification in Liver Disease Types Along the Microbiota-gut-liver Axis.},
journal = {Journal of clinical and experimental hepatology},
volume = {15},
number = {5},
pages = {102552},
pmid = {40292334},
issn = {0973-6883},
abstract = {BACKGROUND: Liver disease, responsible for around two million deaths annually, remains a pressing global health challenge. Microbial interactions within the microbiota-gut-liver axis play a substantial role in the pathogenesis of various liver conditions, including early chronic liver disease (eCLD), chronic liver disease (CLD), acute liver failure (ALF), acute-on-chronic liver failure (ACLF), non-alcoholic fatty liver disease (NAFLD), steatohepatitis, and cirrhosis. This study aimed to identify key molecular signatures involved in liver disease progression by analyzing transcriptomic and gut microbiome data, and to evaluate their diagnostic utility using machine learning models.

METHODS: Transcriptomic analysis identified differentially expressed genes (DEGs) that, when integrated with regulatory elements microRNAs, transcription factors, receptors, and the gut microbiome highlight disease-specific molecular interactions. To assess the diagnostic potential of these molecular signatures, a two-step analysis involving principal component analysis (PCA) and Random Forest classification was conducted, achieving accuracies of 75% for ALF and 89% for NAFLD. Additionally, machine learning algorithms, including K-neighbors, multi-layer perceptron (MLP), decision tree, Random Forest, logistic regression, gradient boosting, CatBoost, Extreme Gradient Boosting (XGB), and Light Gradient Boosting Machine (LGBM), were applied to gene expression data for ALF and NAFLD.

RESULTS: Key genes including CLDN14, EGFR, GSK3B, MYC, and TJP2, alongside regulatory miRNAs let-7a-5p, miR-124-3p, and miR-195-5p and transcription factors NFKB1 and SP1 may be suggested as critical to liver disease progression. Additionally, gut microbiota members, Dictyostelium discoideum and Eikenella might be novel candidates associated with liver disease, highlighting the importance of the gut-liver axis. The Random Forest model reached 75% accuracy and 83% area under the curve for ALF, while NAFLD classification achieved 100% accuracy, precision, recall, and area under the curve underscoring robust diagnostic potential.

CONCLUSION: This study establishes a solid foundation for further research and therapeutic advancement by identifying key biomolecules and pathways critical to liver disease. Additional experimental validation is needed to confirm clinical applicability.},
}

@article {pmid40292324,
year = {2025},
author = {Zhang, R and Li, Z and Huang, L and Kong, W and Zheng, Y and Wang, Y and Shen, X and Huang, L and Wang, X and Zheng, Q and Wu, L and Ke, Y and Mao, R and Peng, Z and Sun, C and Feng, ST and Lin, S and Wang, Y and Li, X},
title = {Altered gut microbiome-metabolite interactions link intestinal inflammation severity and MR enterography abnormalities in Crohn's disease.},
journal = {iScience},
volume = {28},
number = {5},
pages = {112310},
pmid = {40292324},
issn = {2589-0042},
abstract = {Altered gut microbiota‒metabolite interactions may result in intestinal inflammation severity variation in Crohn's disease (CD). Magnetic resonance enterography (MRE) advances anti-inflammatory strategy development. We aimed to identify inflammation-related multiomics factors and MRE interactions for CD management, analyzing 425 CD patients and 42 healthy controls undergoing MRE, ileocolonoscopy, and fecal/blood sampling (microbiota/metabolite analyses), with intestinal inflammation categorized by MRE and ileocolonoscopy. Ruminococcus species were enriched in CD patients versus healthy controls, while Pseudomonas and Staphylococcus dominated moderate-severe versus no-mild inflammation groups, suggesting inflammation-level associations. Ruminococcus gauvreauii suppressed intestinal inflammation by regulating serum PC(O-34:3), ePE(38:6), and ceramides (all p < 0.05). Serum N-acetylneuraminic acid and guanidinoacetic acid correlated with intestinal morphological changes (e.g., MRE-detectable effusion and wall thickness) and inflammation severity (P ACME < 0.05). A link was established between microscopic microbiota-metabolite markers and macroscopic imaging of inflammatory features, which could offer valuable insights into inflammation management.},
}

@article {pmid40292300,
year = {2025},
author = {Pan, Y and Lee, YJ and Kim, JH and Song, MJ and Kwack, K and Park, SH and Sin, SI and Chung, JH and Park, KY},
title = {Suppressor effects of carrots on azoxymethane/dextran sulfate sodium-induced colon cancer according to cultivation method.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1554801},
pmid = {40292300},
issn = {1664-3224},
mesh = {Animals ; *Daucus carota/growth & development ; Mice ; Azoxymethane/toxicity ; Dextran Sulfate/toxicity ; *Colonic Neoplasms/chemically induced/pathology/prevention & control/metabolism ; Apoptosis/drug effects ; Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; Colon/pathology ; Cytokines/metabolism ; },
abstract = {INTRODUCTION: This study investigated the suppressor effects of carrots depending on cultivation method on AOM/DSS-induced colon cancer in mice by examining cell apoptosis, inflammation response, and metabolites. Carrots grown using different fertilizers significantly suppressed tumor development by modulating cell apoptosis and inflammatory responses in our experimental settings.

METHODS AND RESULTS: Naturaldream Fertilizer Carrot (NFC) cultivated with deep sea water minerals (DSWM) showed effectively increased the expression of apoptosis-related genes and proteins including p53, p21, Bim, Bad, Bax, Bak, Caspase 9, and Caspase 3 in colon tissue, while inhibiting the production of inflammatory factors and related genes and proteins such as TNF-a, IL-1b, IL-6, IFN-g, NF-kB, and iNOS in serum, spleen cells, and liver tissues. Intestinal microbiota analysis revealed a distinct composition in mice receiving carrots compared to the control group, with accumulation of intestinal microorganisms such as Lachnospiraceae, and Mucispirillum schaedleri closely associated with anti-tumor effects.

DISCUSSION AND CONCLUSION: Overall, our results indicate that carrots, especially carrots grown with DSWM fertilizers, play a crucial role in inhibiting AOM/DSS-induced colon cancer in mice by regulating cell apoptosis and inflammation responses. The present findings provide valuable insights for further exploration of carrots depending on the cultivation method, as a potential dietary source against colon cancer.},
}

Animals
*Daucus carota/growth & development
Mice
Azoxymethane/toxicity
Dextran Sulfate/toxicity
*Colonic Neoplasms/chemically induced/pathology/prevention & control/metabolism
Apoptosis/drug effects
Gastrointestinal Microbiome
Male
Disease Models, Animal
Colon/pathology
Cytokines/metabolism

@article {pmid40292122,
year = {2025},
author = {Freitag, N and Wienemann, T and Nguyen, TMTL and Höhn, T and Kristin, J and Schramm, D},
title = {Microbial alterations in the lungs of children with chronic pulmonary aspiration.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1520487},
pmid = {40292122},
issn = {2296-2360},
abstract = {INTRODUCTION: Chronic pulmonary aspiration (CPA), a common complication of pediatric dysphagia, poses significant risks to respiratory health, potentially leading to bronchiectasis and permanent lung damage. Despite its clinical impact, the mechanisms underlying aspiration-related lung injury remain unclear. This study investigates the microbial alterations in the lungs of children with CPA and their association with immune responses.

METHODS: We conducted a retrospective analysis of bronchoalveolar lavage fluid (BALF) from children diagnosed with CPA and from controls without swallowing difficulties. Data were collected from patients who underwent bronchoscopy at the University Hospital Düsseldorf between 2010 and 2022. Microbial profiles-including bacterial, viral, and fungal components-and immune cell populations, were assessed to explore the relationship between microbial colonization and immune response in CPA.

RESULTS: The study included 371 children, of whom 48 had CPA. The CPA group exhibited altered microbial colonization, with an increased prevalence of Pseudomonas aeruginosa and Enterobacterales. While the presence of mixed upper respiratory flora did not differ significantly between groups, pathogenic bacteria were more frequently detected in CPA patients. Notably, total leukocyte counts were elevated in the CPA group, yet neutrophilia was absent.

DISCUSSION: Our findings suggest that children with CPA have a distinct lung microbial composition, characterized by increased colonization of Enterobacterales and P. aeruginosa. These microbial changes may contribute to the pathogenesis of aspiration-related lung disease. Further research is needed to determine whether microbial colonization directly contributes to lung damage in and assess long-term consequences.

CONCLUSION: Microbial dysbiosis in the lungs of children with CPA underscores the need for targeted interventions to prevent or mitigate aspiration-related lung disease. A deeper understanding of microbial colonization in CPA may pave the way for novel therapeutic strategies and improved patient outcomes.},
}

@article {pmid40291991,
year = {2025},
author = {Crakes, KR and Questell, L and Soni, S and Suez, J},
title = {Impacts of non-nutritive sweeteners on the human microbiome.},
journal = {Immunometabolism (Cobham, Surrey)},
volume = {7},
number = {2},
pages = {e00060},
pmid = {40291991},
issn = {2633-0407},
abstract = {Replacing sugar with non-nutritive sweeteners (NNS) is a common dietary strategy for reducing the caloric content and glycemic index of foods and beverages. However, the efficacy of this strategy in preventing and managing metabolic syndrome and its associated comorbidities remains uncertain. Human cohort studies suggest that NNS contribute to, rather than prevent, metabolic syndrome, whereas randomized controlled trials yield heterogeneous outcomes, ranging from beneficial to detrimental impacts on cardiometabolic health. The World Health Organization recently issued a conditional recommendation against using NNS, citing the need for additional evidence causally linking sweeteners to health effects. One proposed mechanism through which NNS induce metabolic derangements is through disruption of the gut microbiome, a link strongly supported by evidence in preclinical models. This review summarizes the evidence for similar effects in interventional and observational trials in humans. The limited available data highlight heterogeneity between trials, as some, but not all, find NNS consumption associated with microbiome modulation as well as metabolic effects independent of sweetener type. In other trials, the lack of microbiome changes coincides with the absence of metabolic effects. We discuss the hypothesis that the impacts of NNS on health are personalized and microbiome dependent. Thus, a precision nutrition approach may help resolve the conflicting reports regarding NNS impacts on the microbiome and health. This review also discusses additional factors contributing to study heterogeneity that should be addressed in future clinical trials to clarify the relationship between NNS, the microbiome, and health to better inform dietary guidelines and public health policies.},
}

@article {pmid40291831,
year = {2025},
author = {Kithan-Lundquist, R and McMillan, HM and He, SY and Sundin, GW},
title = {Temporal fruit microbiome and immunity dynamics in postharvest apple (Malus x domestica).},
journal = {Horticulture research},
volume = {12},
number = {6},
pages = {uhaf063},
pmid = {40291831},
issn = {2662-6810},
abstract = {The plant immune response plays a central role in maintaining a well-balanced and healthy microbiome for plant health. However, insights into how the fruit immune response and the fruit microbiome influence fruit health after harvest are limited. We investigated the temporal dynamics of the fruit microbiota and host defense gene expression patterns during postharvest storage of apple fruits at room temperature. Our results demonstrate a temporal dynamic shift in both bacterial and fungal community composition during postharvest storage that coincides with a steep-decline in host defense response gene expression associated with pattern-triggered immunity. We observed the gradual appearance of putative pathogenic/spoilage microbes belonging to genera Alternaria (fungi) and Gluconobacter and Acetobacter (bacteria) at the expense of Sporobolomyces and other genera, which have been suggested to be beneficial for plant hosts. Moreover, artificial induction of pattern-triggered immunity in apple fruit with the flg22 peptide delayed the onset of fruit rot caused by the fungal pathogen Penicillium expansum. Our results suggest that the fruit immune response helps to orchestrate a microbiome and that the collapse of the immunity results in the proliferation of spoilage microbes and fruit rot. These findings hold implications for the development of strategies to increase fruit quality and prolong shelf life in fruits and vegetables.},
}

@article {pmid40291804,
year = {2025},
author = {Wu, Y and Mo, J and Wang, Q and Li, J and Wei, J and Zhang, N and Dong, Y and Zhu, X and Lu, T and Huang, S},
title = {Microbiome and metabolome explain the high-fat diet-induced diabetes development and diabetes resistance in Guizhou mini-pigs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1555069},
pmid = {40291804},
issn = {1664-302X},
abstract = {Type 2 diabetes mellitus (T2DM) is an obesity-related disease claiming substantial global mortality annually. Current animal models of T2DM remain limited, with low success rates in establishing porcine models of high-fat diet (HFD)-induced T2DM. Our experimental design employed 35 Guizhou mini-pigs to develop a T2DM model via HFD induction, aiming to identify microbial and metabolic signatures associated with disease pathogenesis and resistance. At month 10, five individuals from the control (CTR), T2DM (DM), and T2DM resistant (anti-DM) groups were slaughtered, samples were collected, and relevant indices were measured. Metagenomics, metabolomics, and 16S rRNA sequencing were performed to identify microbes and metabolites linked to T2DM progression and resistance. Key findings demonstrated anti-DM group parameters-including metabolic indices (fasting blood glucose, insulin levels, HbA1c, IVGTT), histopathology (HE-stained pancreatic/hepatic tissues), microbial profiles (structural, compositional, functional), and metabolomic signatures-occupied intermediate positions between CTR and DM groups. Network analyses revealed: (1) Lactobacillus, L. amylovorus, fingolimod, polyoxyethylene sorbitan monooleate, thiamine, and atrazine in HFD-associated networks; (2) Limosilactobacillus reuteri, N-oleoyl-L-serine, tolbutamide, tetradecanoyl carnitine, 3'-sulfogalactosylceramide, and guggulsterone in T2DM resistance networks; (3) Ruminococcaceae NK4A214 group, diethyl phthalate, zingerone, enalapril, 5-hydroxytryptophol, 2'-deoxyinosine, icariin, and emetine in T2DM progression networks. These results further clarify the role of the gut microbiota and serum metabolites in the development of T2DM in the Guizhou mini-pig model.},
}

@article {pmid40291803,
year = {2025},
author = {Yang, M and Cai, Y and Bai, T and Han, X and Zeng, R and Liu, D and Liu, T and Liu, R and Ma, C and Yu, L},
title = {Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1512694},
pmid = {40291803},
issn = {1664-302X},
abstract = {INTRODUCTION: Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of the rhizosphere microbiome in tobacco plants infected with Fusarium root rot remain poorly understood.

METHODS: In this study, we analyzed the differences in the compositions and functions of the bacterial and fungal communities in the rhizosphere and root endosphere of healthy tobacco plants and tobacco with Fusarium root rot using amplicon sequencing and metagenomic sequencing.

RESULTS AND DISCUSSION: Our results showed that Fusarium root rot disrupted the stability of bacteria-fungi interkingdom networks and reduced the network complexity. Compared to healthy tobacco plants, the Chao1 index of bacterial communities in the rhizosphere soil of diseased plants increased by 4.09% (P < 0.05), while the Shannon and Chao1 indices of fungal communities decreased by 13.87 and 8.17%, respectively (P < 0.05). In the root tissues of diseased plants, the Shannon index of bacterial and fungal communities decreased by 17.71-27.05% (P < 0.05). Additionally, we observed that the rhizosphere microbial community of diseased tobacco plants shifted toward a pathological combination, with a significant increase in the relative abundance of harmful microbes such as Alternaria, Fusarium, and Filobasidium (89.46-921.29%) and a notable decrease in the relative abundance of beneficial microbes such as Lysobacter, Streptomyces, Mortierella, and Penicillium (48.48-81.56%). Metagenomic analysis further revealed that the tobacco rhizosphere microbial communities of diseased plants played a significant role in basic biological metabolism, energy production and conversion, signal transduction, and N metabolism, but their functions involved in C metabolism were significantly weakened. Our findings provide new insights into the changes in and interactions within the rhizosphere and root endosphere microbiomes of tobacco plants under the stress of Fusarium soil-borne fungal pathogens, while laying the foundation for the exploration, development, and utilization of beneficial microbial resources in healthy tobacco plants in the future.},
}

@article {pmid40291383,
year = {2025},
author = {Ablin, JN},
title = {Fibromyalgia: are you a genetic/environmental disease?.},
journal = {Pain reports},
volume = {10},
number = {3},
pages = {e1256},
pmid = {40291383},
issn = {2471-2531},
abstract = {Fibromyalgia, characterized by chronic widespread pain and fatigue, involves complex interactions between genetic predispositions and environmental triggers. This review delves into the multifaceted nature of fibromyalgia, emphasizing recent advances in understanding its pathogenesis through genetic, epigenetic, and environmental lenses. We explore the roles of specific genetic polymorphisms, such as those in the catechol-O-methyltransferase and serotonin transporter genes, and their correlation with the syndrome's susceptibility. The review also examines the significant impact of environmental factors, including physical trauma and stress, which potentiate the syndrome's severity. In addition, emerging research on the microbiome and epigenetic modifications provides new insights into the disease mechanisms, potentially guiding future therapeutic strategies. This article aims to synthesize current research findings and propose directions for future research, underscoring the necessity of a multidisciplinary approach to decipher the complexities of fibromyalgia.},
}

@article {pmid40291282,
year = {2025},
author = {Tanemura, S and Mima, Y},
title = {A Case of Cutaneous Fungal Infection Following the Administration of Dupilumab.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e81349},
pmid = {40291282},
issn = {2168-8184},
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin condition with a multifactorial etiology. Herein, we report a case of a patient with AD undergoing long-term topical treatments who developed a dermatophyte infection following the administration of dupilumab. Dupilumab is known to enhance skin barrier function and induce changes in the skin microbiome. Notably, head and neck dermatitis caused by the overgrowth of Malassezia species due to dupilumab has been widely discussed. This phenomenon is thought to result from the suppression of T helper (Th)2 cytokines by dupilumab, leading to a decrease in the proportion of Staphylococcus aureus and a relative increase in fungal populations. Additionally, feedback activation of Th17 cytokines may trigger excessive inflammation against fungi, contributing to fungal infections. IL-13 plays critical roles in fungal colony formation, and tralokinumab, an IL-13 inhibitor, has shown potential efficacy in treating this head and neck dermatitis. While the relationship between microbiome changes and biologics like lebrikizumab and nemolizumab remains unexplored, investigating the differential effects of these therapies on the cutaneous microbiome could provide deeper insights into not only the unique characteristics of each biologic agent but also the roles of Th2 cytokines such as IL-4, IL-13, and IL-31 in the pathophysiology of AD. The present case underscores the importance of the comprehensive therapeutic approach for AD that accounts for microbiome dynamics and adapts to evolving skin changes throughout the course of treatment.},
}

@article {pmid40291231,
year = {2025},
author = {Zim, A and Bommareddy, A},
title = {Estrogen-Gut-Brain Axis: Examining the Role of Combined Oral Contraceptives on Mental Health Through Their Impact on the Gut Microbiome.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e81354},
pmid = {40291231},
issn = {2168-8184},
abstract = {Combined oral contraceptives (COCs) possess the ability to alter the normal composition of the gut microbiome and the permeability of the gastrointestinal (GI) tract, which may cause both gut-related and non-gut-related complications. The gut-estrogen axis examines the relationship between estrogens (particularly the active form, estradiol) and the gastrointestinal system and can be attributed to the maintenance of the estrobolome and circulating estradiol levels. The gut-brain axis involves the relationship between the brain and the gastrointestinal system and can be attributed to the gut microbiome in relation to the enteric nervous system (ENS) and serotonin levels. Overall, the introduction of exogenous hormones into an endogenous environment alters the normal balance of both hormones and bacteria. Currently, there is a gap in knowledge regarding the link between COCs and mental health complications such as anxiety and depression, and the diversity in these complications may be related to different types of COCs, their composition, and variations in study populations. This article reviews existing evidence from animal and human studies on the role of COCs in the development of mental health issues through their impact on the gut microbiome.},
}

@article {pmid40290694,
year = {2025},
author = {Shen, TH and Yu, X and Zhou, C and Liu, Y and Li, QY and Li, W and Jiang, TH and Zhu, YQ and Liu, Y},
title = {Review of the mechanisms of the biliary-enteric axis in the development of cholangiocarcinoma.},
journal = {World journal of clinical oncology},
volume = {16},
number = {4},
pages = {102374},
pmid = {40290694},
issn = {2218-4333},
abstract = {Cholangiocarcinoma (CCA) is a particularly aggressive and challenging type of cancer, known for its poor prognosis, which is worsened by the complex interplay of various biological and environmental factors that contribute to its development. Recently, researchers have increasingly focused on the significant role of the biliary-enteric communication of liver-gut axis in the pathogenesis of CCA, highlighting a complex relationship that has not been thoroughly explored before. This review aims to summarize the key concepts related to the biliary-enteric communication of liver-gut axis and investigate its potential mechanisms that may lead to the onset and progression of CCA, a disease that presents substantial treatment challenges. Important areas of focus will include the microbiome's profound influence, which interacts with host physiology in ways that may worsen cancer development; changes in bile acid metabolism that can create toxic environments favorable for tumor growth; the regulation of inflammatory processes that may either promote or inhibit tumor progression; the immune system's involvement, which is crucial in the body's response to cancer; and the complex interactions within metabolic pathways that can affect cellular behavior and tumor dynamics. By integrating recent research findings from various studies, we aim to explore the multifaceted roles of the biliary-enteric communication of liver-gut axis in CCA, providing new insights and perspectives for future research while identifying promising therapeutic targets that could lead to innovative treatment strategies aimed at improving patient outcomes in this challenging disease.},
}

@article {pmid40290663,
year = {2025},
author = {Shokri, S and Jarpa-Parra, M},
title = {Editorial: Advancements in protein modification for enhanced digestibility.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1603394},
pmid = {40290663},
issn = {2296-861X},
}

@article {pmid40290371,
year = {2025},
author = {Kang, A and Eor, JY and Lee, J and Kwak, MJ and Lee, DJ and Seo, E and Lee, WJ and Son, SH and Song, M and Kim, JM and Kim, HW and Yang, J and Oh, S and Kim, Y},
title = {Lacticaseibacillus casei IDCC 3451 alleviates cognitive and behavioral functions by reshaping the gut microbiome and regulating intestinal barrier integrity in chronic stress animal models.},
journal = {Current research in food science},
volume = {10},
number = {},
pages = {101051},
pmid = {40290371},
issn = {2665-9271},
abstract = {Lacticaseibacillus casei IDCC 3451 (3451) was evaluated for its effects on the gut-brain axis using Caenorhabditis elegans (C. elegans) and mouse models of stress and inflammation. In C. elegans, 3451 extended lifespans by 25 %, improved motility, and chemotaxis, enhanced survival under pathogen challenge, and reduced amyloid beta accumulation by 42 %. Transcriptomic profiling revealed upregulation of genes involved in neurotransmitter signaling and serine/threonine pathways. In the unpredictable chronic mild stress (UCMS) mouse model, 3451 administration increased the time spent in the center of the open field by 65 % and reduced immobility in the forced swim test by 32 %, indicating anxiolytic and antidepressant effects. Serum levels of aspartate aminotransferase (AST) and gamma-glutamyl transferase (GGT) were decreased by 18 % and 24 %, respectively. Additionally, 3451 restored the expressions of 5HT1AR, GABAR, and tight junction proteins, including ZO-1 and Claudin1. Metabolomic analysis showed increased glycine and decreased palmitic acid levels, associated with an increased abundance of Ruminococcus and Akkermansia. In the dextran sulfate sodium (DSS)-induced colitis model, 3451 reduced the disease activity index by 36 %, improved colon histology, increased goblet cell preservation, and upregulated ZO-1 and IL-10 expression. Threonine levels were also increased and correlated with a higher abundance of Coprococcus. These findings demonstrate that 3451 improved behavioral and intestinal outcomes through coordinated modulation of host signaling, metabolite production, and gut microbial composition, highlighting its therapeutic potential for managing IBD and neurobehavioral disorders.},
}

@article {pmid40290153,
year = {2025},
author = {Lüthy, L and Thies, LGS and Beitl, KN and Hansen, M and McManus, J and Afzal, M and Schrangl, L and Bloch, S and Subbiahdoss, G and Reimhult, E and Schäffer, C and Carreira, EM},
title = {Synthesis, Microbiology, and Biophysical Characterization of Mutanofactins from the Human Oral Microbiome.},
journal = {ACS central science},
volume = {11},
number = {4},
pages = {601-611},
pmid = {40290153},
issn = {2374-7943},
abstract = {Mutanofactins are a family of natural products produced by Streptococcus mutans from the human oral microbiome. We report a unified approach to all mutanofactins by developing a total synthesis amenable to diversification. The key to success for the most complex members, mutanofactins 607 and 697, was an acyl ketene based strategy. Access to the family enabled comprehensive biological profiling, where we demonstrate that all mutanofactins are biofilm promoting in Streptococcus mutans. Experiments were extended to other inhabitants of the oral microbiome for the first time: Streptococcus gordonii and Streptococcus oralis, two early colonizers, were similarly affected with mutanofactins being biofilm promoting. Conversely, Veillonella dispar and Fusobacterium nucleatum showed little to no reaction to mutanofactins. Biophysical investigations based on quartz crystal microbalance with dissipation monitoring and atomic force microscopy reveal a previously unknown mucin-mutanofactin 697 interaction. Incubation of a mucin layer with mutanofactin 697 induces a morphology change within the mucin layer, which promotes bacterial adhesion and biofilm formation. This unique property of mutanofactin 697 might be key to early stages of biofilm formation in the human oral microbiome. Combined, an interdisciplinary approach consisting of total synthesis, microbiology and biophysical characterization provides insight into the roles of mutanofactins in the oral microbiome.},
}

@article {pmid40290143,
year = {2025},
author = {Yao, ML and Zhang, W},
title = {Where Molecules Meet Mucus: Mutanofactins in the Oral Microbiome.},
journal = {ACS central science},
volume = {11},
number = {4},
pages = {508-510},
pmid = {40290143},
issn = {2374-7943},
}

@article {pmid40290087,
year = {2025},
author = {Aggeletopoulou, I and Geramoutsos, G and Pastras, P and Triantos, C},
title = {Vitamin D in Irritable Bowel Syndrome: Exploring Its Role in Symptom Relief and Pathophysiology.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17061028},
pmid = {40290087},
issn = {2072-6643},
mesh = {Humans ; *Irritable Bowel Syndrome/physiopathology/drug therapy ; *Vitamin D/therapeutic use/administration & dosage ; Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; *Vitamin D Deficiency/complications/physiopathology/drug therapy ; Quality of Life ; },
abstract = {Irritable Bowel Syndrome (IBS) is a chronic functional gastrointestinal disorder. Despite its common occurrence, the pathophysiology of IBS remains not fully understood. Emerging evidence suggests that IBS is a multifactorial condition characterized by low-grade inflammation, immune system activation, impaired gut permeability, intestinal hypersensitivity, and alterations in intestinal microbiota. Recent data have highlighted the potential role of vitamin D in modulating these underlying mechanisms. Vitamin D is known to influence various cellular processes, including the regulation of the gut microbiome, immune response modulation, and anti-inflammatory effects, which may alleviate the altered gut function observed in IBS. Research indicates that individuals with IBS often have lower levels of vitamin D compared to healthy controls, suggesting a possible link between vitamin D deficiency and IBS. Vitamin D supplementation has been associated with improvements in IBS symptoms, such as bloating, flatulence, abdominal pain, constipation, and overall quality of life. The mechanisms by which vitamin D exerts these effects may involve direct or indirect modulation of immune responses, the production of antimicrobial peptides, and the regulation of gene expression related to serotonergic metabolism. Despite these promising findings, the exact pathways through which vitamin D affects IBS pathophysiology remain unclear. The aim of this review is to outline the current knowledge and evidence regarding these mechanisms, as well as the therapeutic potential of vitamin D supplementation in IBS patients. Exploring the connection between vitamin D and IBS may pave the way for innovative interventions, enhancing both management strategies and the quality of life for those affected by the disorder.},
}

Humans
*Irritable Bowel Syndrome/physiopathology/drug therapy
*Vitamin D/therapeutic use/administration & dosage
Gastrointestinal Microbiome/drug effects
Dietary Supplements
*Vitamin D Deficiency/complications/physiopathology/drug therapy
Quality of Life

@article {pmid40290056,
year = {2025},
author = {Wang, T and Langendijk, P and Azevedo, P and Fabà, L and Zuo, B and Zhao, J and Yang, C},
title = {Effects of fiber concentrations and fermentation rates on reproductive performance, nutrient digestibility, immune response and microbiota of lactating sows.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf110},
pmid = {40290056},
issn = {1525-3163},
abstract = {Certain types of fiber inclusion in sow diets can offer benefits such as promoting a healthy microbiome, improving intestinal health, and enhancing welfare through satiety mechanisms. While most research has focused on gestating sows, studies on lactating sows, especially regarding fiber types, levels, and fermentation rates, are limited. This study explored how fiber inclusion and fermentation rate affect lactation performance, nutrient digestibility, immune response, and microbiota. The study involved 136 lactating sows (Landrace × Large White) assigned to four dietary treatments with varying total dietary fiber (TDF) levels and proportions of fast fermentable fiber. Diets 1 and 2 had low TDF (15%), while Diets 3 and 4 had high TDF (25%). Fast fermentable fiber was included at 1.25% and 2.5% in the low fiber diets, and at 3.75% and 5% in the high fiber diets. Fiber sources like sugar beet pulp, oat hulls, wheat millrun, and barley were used based on their fermentable fiber proportions, measured using an in-house Trouw Nutrition assay. Effective energy (EE), crude protein (CP), and lysine contents were consistent across diets. Sows were fed starting at 3 kg/d (primiparous) or 3.5 kg/d (multiparous), increasing to 7 kg/d or 8 kg/d by 8 or 9 days post-farrowing. High fiber diets reduced apparent total tract digestibility (ATTD) of nutrients (P < 0.001) but increased sow fat loss (P < 0.05). Sows consuming fast fermentable fiber had lower body weight and protein loss (P < 0.05), decreased serum interleukin-8 (IL-8) levels (P < 0.05), and improved ATTD of gross energy (GE) (P = 0.016), dry matter (DM) on day 19 (P < 0.001), CP (P < 0.001), and nitrogen (P < 0.001) and a trend toward higher fat levels in milk (P = 0.099). High fiber diets decreased microbiota diversity but increased beneficial families such as Prevotellaceae, Ruminococcaceae, and Lachnospiraceae. Although high fiber diets lowered ATTD of nutrients, feeding these diets during lactation improved sow performance without negatively affecting feed intake, milk composition, microbiota, and did not impact litter weaning weight. Fast fermentable fiber also reduced IL-8 levels, body weight loss, and protein loss, suggesting it benefits lactating sows.},
}

@article {pmid40290041,
year = {2025},
author = {Na, JH and Lee, H and Lee, YM},
title = {Clinical Efficacy and Safety of the Ketogenic Diet in Patients with Genetic Confirmation of Drug-Resistant Epilepsy.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17060979},
pmid = {40290041},
issn = {2072-6643},
support = {6-2024-0101//a faculty research grant from the Yonsei University College of Medicine/ ; },
mesh = {Humans ; *Diet, Ketogenic/methods/adverse effects ; *Drug Resistant Epilepsy/diet therapy/genetics ; Treatment Outcome ; },
abstract = {Drug-resistant epilepsy (DRE) affects 20-30% of patients with epilepsy who fail to achieve seizure control with antiseizure medications, posing a significant therapeutic challenge. In this narrative review, we examine the clinical efficacy and safety of the classic ketogenic diet (cKD) and its variants, including the modified Atkins diet (MAD), medium-chain triglyceride diet (MCTD), and low glycemic index treatment (LGIT), in patients with genetically confirmed drug-resistant epilepsy. These diets induce a metabolic shift from glucose to ketones, enhance mitochondrial function, modulate neurotransmitter balance, and exert anti-inflammatory effects. However, genetic factors strongly influence the efficacy and safety of the cKD, with absolute indications including glucose transporter type 1 deficiency syndrome (GLUT1DS) and pyruvate dehydrogenase complex deficiency (PDCD). Preferred adjunctive applications of the KD include genetic epilepsies, such as SCN1A-related Dravet syndrome, TSC1/TSC2-related tuberous sclerosis complex, and UBE3A-related Angelman syndrome. However, because of the risk of metabolic decompensation, the cKD is contraindicated in patients with pathogenic variants of pyruvate carboxylase and SLC22A5. Recent advancements in precision medicine suggest that genetic and microbiome profiling may refine patient selection and optimize KD-based dietary interventions. Genome-wide association studies and multiomics approaches have identified key metabolic pathways influencing the response to the cKD, and these pave the way for individualized treatment strategies. Future research should integrate genomic, metabolomic, and microbiome data to develop biomarker-driven dietary protocols with improved efficacy and safety. As dietary therapies continue to evolve, a personalized medical approach is essential to maximize their clinical utility for genetic epilepsy and refractory epilepsy syndromes.},
}

Humans
*Diet, Ketogenic/methods/adverse effects
*Drug Resistant Epilepsy/diet therapy/genetics
Treatment Outcome

@article {pmid40290029,
year = {2025},
author = {Thomas, KL and Wahlquist, AE and James, D and Clark, WA and Wagner, CL},
title = {Effects of Maternal Pre-Pregnancy BMI on Preterm Infant Microbiome and Fecal Fermentation Profile-A Preliminary Cohort Study.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17060987},
pmid = {40290029},
issn = {2072-6643},
support = {RDC//ETSU/ ; },
mesh = {Humans ; Female ; *Feces/microbiology ; Pregnancy ; *Body Mass Index ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome ; Adult ; *Fermentation ; Cohort Studies ; Fatty Acids, Volatile/analysis/metabolism ; Obesity/microbiology ; Male ; Overweight/microbiology ; },
abstract = {Objective: This feasibility, proof-of-concept study aimed to assess the impact of maternal pre-pregnancy body mass index (BMI) on preterm infant fecal fermentation and microbiome. Study Design: An infant cohort study (n = 54) in the NICU at MUSC from June 2021 to September 2022 was grouped according to maternal pre-pregnancy BMI-normal weight (<25 kg/m[2]), overweight (25-29.9 kg/m[2]), and obese (≥30 kg/m[2]). All fecal samples were subjected to 16s rRNA isolation and analysis, as well as short chain fatty acid (SCFA) extraction and analysis. Results: Preterm infants born to overweight and obese mothers did not have differences in microbial diversities but did have different bacterial taxonomic composition and lower relative abundance levels of taxa than those born to normal-weight mothers. While controlling for covariates, we found SCFA propionic acid to be higher and more significant in infant stools born to mothers with a higher pre-pregnancy BMI. Conclusions: This is a novel study investigating the microbiome and SCFA in premature infants while considering maternal pre-pregnancy BMI. This study adds to the current literature, in that the preterm infant gut is generally lower in microbial diversity which can impact infant health. Thus, it is important to understand the mechanisms necessary to modulate the microbiome of preterm infants to improve their health outcomes.},
}

Humans
Female
*Feces/microbiology
Pregnancy
*Body Mass Index
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome
Adult
*Fermentation
Cohort Studies
Fatty Acids, Volatile/analysis/metabolism
Obesity/microbiology
Male
Overweight/microbiology

@article {pmid40290019,
year = {2025},
author = {Lazarini, T and Tonon, KM and Araujo Filho, HB and Morais, MB},
title = {Bifidogenic Effect of 2'-Fucosyllactose (2'-FL) on the Gut Microbiome of Healthy Formula-Fed Infants: A Randomized Clinical Trial.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17060973},
pmid = {40290019},
issn = {2072-6643},
support = {0000//Nestlé (Brazil)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Infant Formula/chemistry ; *Trisaccharides/pharmacology/administration & dosage ; Infant ; *Prebiotics/administration & dosage ; Feces/microbiology ; Female ; Male ; Oligosaccharides/pharmacology/administration & dosage ; Milk, Human/chemistry ; Breast Feeding ; Bifidobacterium ; RNA, Ribosomal, 16S ; },
abstract = {Breast milk is rich in bioactive components, especially human milk oligosaccharides (HMOs), which are crucial for establishing gut microbiota. The 2'-FL (2-Fucosyllactose), one of the most abundant oligosaccharides in breast milk, functions as a selective prebiotic. Objective: To examine the effect of adding 2'-FL (2-Fucosyllactose) to an infant formula containing prebiotic galacto-oligosaccharides (GOSs) and fructo-oligosaccharides (FOSs) on the gut microbiome of healthy formula-fed infants. Methods: This study enrolled infants from three groups: an HMO experimental group (n = 29), a GOS/FOS control group (n = 30), and an exclusively breastfed (breast milk [BM]) reference group (n = 28). Fecal samples from the three groups in the first and fourth months of life were analyzed. The V3 and V4 regions of the 16S rRNA gene were amplified and sequenced on the Illumina MiSeq. ANOVA, Kruskal-Wallis, richness indices (Chao1, Shannon), UniFrac distances, and the Adonis tests were used to perform statistical analyses on the relative abundance of phyla and genera, as well as the alpha and beta-diversity of the gut microbiota. Results: After intervention, Actinobacteriota emerged as the predominant phylum in both the HMO (60.4%) and BM (46.6%) groups. Bifidobacterium and Escherichia-Shigella were identified as the two most abundant bacterial genera in both groups. Nevertheless, the statistical analysis showed that the relative abundance of Bifidobacterium in the HMO formula-fed group after intervention was similar to that in the BM group (p > 0.05). Infants in the HMO and GOS/FOS groups showed higher relative abundance of [Ruminococcus]_gnavus_group bacteria compared to those in the BM group. Groups fed with infant formula demonstrated higher alpha-diversity of gut microbiota compared to breastfed infants (p < 0.05), at the time of admission as well as after the intervention. Beta-diversity was significantly different among the three groups, according to type of feeding. Infants fed a 2'-FL-supplemented infant formula exhibited growth comparable to that of breastfed infants throughout the intervention period, demonstrating that the formula was both safe and well tolerated. Conclusions: Adding 2'-FL to an infant formula containing 4 g/L of GOS + FOS resulted in a stronger bifidogenic effect compared to the formula without 2'-FL.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Infant Formula/chemistry
*Trisaccharides/pharmacology/administration & dosage
Infant
*Prebiotics/administration & dosage
Feces/microbiology
Female
Male
Oligosaccharides/pharmacology/administration & dosage
Milk, Human/chemistry
Breast Feeding
Bifidobacterium
RNA, Ribosomal, 16S

@article {pmid40289936,
year = {2025},
author = {Maltz, S and Nacey, AT and Maury, J and Ghanem, N and Lee, SY and Aquilino, TM and Graham, EL and Wrigley, SD and Whittington, JM and Khandaker, AM and Hart, RA and Byrne, L and Wei, Y and Pradelles, R and Johnson, SA and Weir, TL},
title = {Effects of Supplementation with Microalgae Extract from Tetradesmus obliquus Strain Mi175.B1.a on Gastrointestinal Symptoms and Mental Health in Healthy Adults: A Pilot Randomized, Double-Blind, Placebo-Controlled, Parallel-Arm Trial.},
journal = {Nutrients},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/nu17060960},
pmid = {40289936},
issn = {2072-6643},
support = {N/A//Microphyt/ ; },
mesh = {Humans ; Double-Blind Method ; Adult ; Male ; Female ; *Dietary Supplements ; Pilot Projects ; *Microalgae/chemistry ; Anxiety ; *Gastrointestinal Diseases ; *Mental Health ; Healthy Volunteers ; Stress, Psychological ; Young Adult ; Biomarkers/blood ; Feces/chemistry ; },
abstract = {Microalgae, a marine-derived natural ingredient, has emerged as a rich source of bioactive compounds with the potential to modulate gut-brain axis activities. The objective of this study was to investigate whether supplementation with a microalgae extract from Tetradesmus obliquus strain Mi175.B1.a (TOME) influences gut health and reduces stress and anxiety in healthy adults experiencing mild to moderate gastrointestinal (GI) distress. Methods: Fifty-six healthy adults (age: 31.9 ± 7.7 years; body weight: 71.8 ± 12.6 kg; BMI: 24.6 ± 2.8 kg/m[2]) were enrolled in a randomized, double-blind, placebo-controlled, parallel-arm clinical trial. Participants were randomly allocated to receive capsules containing either 250 mg/day of TOME or a placebo for four weeks. Primary outcomes included the assessment of GI symptoms using the Gastrointestinal Symptom Rating Scale (GSRS) and Bristol Stool Scale (BSS). Secondary outcomes focused on subjective evaluation of mood, stress, and anxiety, as well as blood pressure responses to sympathetic nervous system activation induced by the cold pressor test (CPT). In addition, stool, plasma, and saliva samples were collected to assess biomarkers associated with stress, sympathetic activation, intestinal permeability, and GI health. 16S rRNA sequencing was performed to analyze changes in gut microbial populations. Results: Daily supplementation for four weeks with TOME was safe and well tolerated in the study population. In addition, TOME significantly reduced GSRS global scores (p = 0.02), as well as constipation (p = 0.05) and indigestion (p = 0.03) subcomponent scores compared to Placebo. There was also a significant increase in Shannon's index before FDR correction (p = 0.05; FDR = 0.12) and stool butyrate level was significantly lower in the TOME group than in Placebo after 4 weeks of supplementation (p = 0.039). Both groups showed a significant reduction in perceived stress scores, but the TOME intervention group also had reduced Negative Affect scores (p < 0.001). In addition, plasma chromogranin A, a stress biomarker, was significantly reduced after TOME intervention (p = 0.03). There were no negative effects on blood lipids or other parameters related to sympathetic activation or cardiovascular health. Conclusions: Overall, these results suggest that 4-week supplementation with T. obliquus strain Mi175.B1.a improves GI symptoms, potentially through effects on the gut microbiota, and may promote positive effects on mental health. Additional research should follow up on mental health outcomes in populations with increased stress and anxiety and investigate mechanisms underlying improvements in GI health. This trial was registered at clinicaltrials.gov as NCT06425094.},
}

Humans
Double-Blind Method
Adult
Male
Female
*Dietary Supplements
Pilot Projects
*Microalgae/chemistry
Anxiety
*Gastrointestinal Diseases
*Mental Health
Healthy Volunteers
Stress, Psychological
Young Adult
Biomarkers/blood
Feces/chemistry

@article {pmid40289872,
year = {2025},
author = {Gao, L and Zhang, Y and Hu, Z and Chen, S and Wang, Q and Zeng, Y and Yin, H and Zhao, J and Zhan, Y and Gao, C and Xin, Y and Chen, B and van der Veen, S and Zhao, M and Fang, D and Lu, Q},
title = {Microbiota-Derived Inosine Suppresses Systemic Autoimmunity via Restriction of B Cell Differentiation and Migration.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2409837},
doi = {10.1002/advs.202409837},
pmid = {40289872},
issn = {2198-3844},
support = {2022YFC3601800//National Key R&D Program of China/ ; 32141004//Special Program of National Natural Science Foundation of China/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences (CIFMS) No/ ; 2024-I2M-ZH-020//CAMS Innovation Fund for Medical Sciences (CIFMS) No/ ; 2020-RC320-003//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; NO.82430102//Key Program of the National Natural Science Foundation of China/ ; 82404154//National Natural Science Foundation of China/ ; },
abstract = {The role of gut microbiota dysbiosis in systemic lupus erythematosus (SLE) pathogenesis remains elusive. Here, it is shown that fecal microbiota transplantation (FMT) from healthy mice to lupus mice ameliorates lupus-like symptoms. Microbiota reconstitution effectively reduces systemic class switch recombination (CSR) and elevates immunoglobulin heavy chain (IGH) naïve isotype. Microbiota profiling reveals an enrichment of Lactobacillus johnsonii post-FMT, with a significant correlation to purine metabolites. Importantly, the L. johnsonii-derived inosine, an intermediate metabolite in purine metabolism, effectively alleviates lupus pathogenesis in mice. Inosine inhibits B cell differentiation and reduces renal B cell infiltration to protect mice from lupus. At the molecular level, inosine reprograms B cells through the eDDxtracellular signal-regulated kinase (ERK)-hypoxia-inducible factor-1alpha (HIF-1α) signaling pathway. Therefore, this study highlights the discovery of a novel microbial metabolite modulating autoimmunity and suggests its potential for innovative microbiome-based therapeutic approaches.},
}

@article {pmid40289691,
year = {2025},
author = {Giacomini, A and Lakim, MB and Tuh, FYY and Hitchings, M and Consuegra, S and Webster, TU and Wells, K},
title = {Host-Microbiome Associations of Native and Invasive Small Mammals Across a Tropical Urban-Rural Ecotone.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17782},
doi = {10.1111/mec.17782},
pmid = {40289691},
issn = {1365-294X},
support = {IF\R1\231030//Royal Society Industry Fellowship/ ; //Swansea University FSE postgraduate research scholarship/ ; },
abstract = {Global change and urbanisation profoundly alter wildlife habitats, driving native animals into novel habitats while increasing the co-occurrence between native and invasive species. Host-microbiome associations are shaped by host traits and environmental features, but little is known about their plasticity in co-occurring native and invasive species across urban-rural gradients. Here, we explored gut microbiomes of four sympatric small mammal species along an urban-rural ecotone in Borneo, one of the planet's oldest rainforest regions experiencing recent urban expansion. Host species identity was the strongest determinant of microbiome composition, while land use and spatial proximity shaped microbiome similarity within and among the three rat species. The urban-dwelling rat Rattus rattus had a microbiome composition more similar to that of the native, urban-adapted rat Sundamys muelleri (R. rattus' strongest environmental niche overlap), than to the closely related urban-dwelling R. norvegicus. The urban-dwelling shrew Suncus murinus presented the most distinct microbiome. The microbiome of R. norvegicus was the most sensitive to land use intensity, exhibiting significant alterations in composition and bacterial abundance across the ecotone. Our findings suggest that environmental niche overlap among native and invasive species promotes similar gut microbiomes. Even for omnivorous urban-dwellers with a worldwide distribution like R. norvegicus, gut microbiomes may change across fine-scale environmental gradients. Future research needs to confirm whether land use intensity can be a strong selective force on mammalian gut microbiomes, influencing the way in which native and invasive species are able to exploit novel environments.},
}

@article {pmid40289657,
year = {2025},
author = {Qu, Y and Liu, X and Su, Z and Guo, Q and Ma, P},
title = {Suppressiveness of spent mushroom substrate amendment against eggplant Verticillium wilt.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.8799},
pmid = {40289657},
issn = {1526-4998},
support = {32172487//National Natural Science Foundation of China/ ; 32102284//National Natural Science Foundation of China/ ; 2022KJCXZX-ZBS-1//HAAFS Science and Technology Innovation Special Project/ ; 2023KJCXZX-ZBS-GH01//HAAFS Science and Technology Innovation Special Project/ ; 2023120102//Basic Research Funds of Hebei Academy of Agriculture and Forestry Sciences/ ; },
abstract = {BACKGROUND: Verticillium wilt, caused by Verticillium dahliae, is a devastating soil-borne disease. Spent mushroom substrate (SMS) has shown potential as a soil amendment for controlling soil-borne diseases. However, the mechanisms underlying its disease-suppressive effects remain poorly understood. Here, the efficacy of SMS in suppressing eggplant Verticillium wilt and mechanisms related to rhizosphere microbiome regulation were investigated.

RESULTS: We tested different SMS sources (Pleurotus ostreatus, Hypsizygus marmoreus, Lentinus edodes), particle sizes (45, 75, 150, 300 μm), and addition ratios (0.5-8%, w/w). The fungus control efficacy ranged from 26 to 66%, with best results from 2% SMS of L. edodes at 150 μm. This treatment resulted in 5.7-fold reduction in the Verticillium dahliae population in eggplant rhizosphere. Eggplant fresh and dry weights of shoots and roots, and plant height, significantly increased with 2% SMS amendment. 16S rDNA sequencing revealed alterations in rhizosphere bacterial communities, with an increase in indigenous beneficial bacteria, particularly Bacillus spp., following SMS amendment. Spent mushroom substrate co-inoculated with exogenous biocontrol strain Bacillus subtilis NCD-2 achieved a synergistic effect against Verticillium wilt than both SMS or NCD-2 alone.

CONCLUSIONS: Results revealed that SMS protects eggplants against Verticillium wilt, largely by recruiting Bacillus spp. to the rhizosphere. The enrichment effect of indigenous Bacillus spp. in the rhizosphere mediated by SMS similarly applies to Bacillus inoculum, enhancing its efficacy in controlling eggplant Verticillium wilt. These findings enhance our understanding of the protective effects of SMS and its role in the biocontrol of Verticillium wilt. © 2025 Society of Chemical Industry.},
}

@article {pmid40289407,
year = {2025},
author = {Aho, VTE and Clerbaux, LA and Kupczok, A and Tillett, B and Garg, N and Henderickx, JGE},
title = {A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e202500019},
doi = {10.1002/pmic.202500019},
pmid = {40289407},
issn = {1615-9861},
abstract = {Metaproteomics, an emerging field among the omic techniques, holds great promise for unraveling the function of microbiomes in host health and our environment. Metaproteomics can also be a valuable addition to multiomics studies of the microbiome, complementing genome-resolved metagenomics, metatranscriptomics, and metabolomics. The potential advancements from metaproteomics and multiomics research touch a breadth of disciplines, including ecology, biochemistry, immunology, medical microbiology, cell physiology, and medicine, and could lead to both fundamental and applied discoveries. However, there are significant roadblocks to widespread adoption of metaproteomics among microbiome researchers. In this Viewpoint article, we highlight the pivotal role of metaproteomics in microbiome research by showcasing its advantages, exploring opportunities to overcome challenges, and paving the way for its broader adoption as a mainstream technique. We hope that the recommendations provided in this Viewpoint article will inspire new, beneficial collaborations between proteomics experts, algorithm and infrastructure developers, biochemists, cell biologists, and microbiologists, enabling the construction of a knowledge base of microbiome function that can have an immediate and direct impact on host health and the environment.},
}

@article {pmid40289251,
year = {2025},
author = {Slager, J and Simpson, HL and Gacesa, R and Chen, L and Tan, IL and Gelderloos, J and Maatman, A and Wijmenga, C and Zhernakova, A and Fu, J and Weersma, RK and Gonera, G and Jonkers, IH and Withoff, S},
title = {High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2489071},
doi = {10.1080/19490976.2025.2489071},
pmid = {40289251},
issn = {1949-0984},
mesh = {Humans ; *Celiac Disease/microbiology/diet therapy ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Middle Aged ; Adult ; Netherlands ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; Aged ; },
abstract = {BACKGROUND: Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterized by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and environmental factors. While recent data show that alterations in gut microbiome composition could play an important role, many current studies are constrained by small sample sizes and limited resolution.

METHODS: To address these limitations, we analyzed fecal gut microbiota from two Dutch cohorts, CeDNN (128 treated CeD patients (tCeD), 106 controls) and the Lifelines Dutch Microbiome Project (24 self-reported tCeD, 654 controls), using shotgun metagenomic sequencing. Self-reported IBS (570 cases, 1710 controls) and IBD (93 cases, 465 controls) were used as comparative conditions of the gastrointestinal tract. Interindividual variation within the case and control groups was calculated at whole microbiome and strain level. Finally, species-specific gene repertoires were analyzed in tCeD patients and controls.

RESULTS: Within-individual microbiome diversity was decreased in patients with self-reported IBS and IBD but not in tCeD patients. Each condition displayed a unique microbial pattern and, in addition to confirming previously reported microbiome associations, we identify an increase in the levels of Clostridium sp. CAG:253, Roseburia hominis, and Eggerthella lenta, amongst others. We further show that the observed changes can partially be explained by gluten-free diet adherence. We also observe increased interindividual variation of gut microbiome composition among tCeD patients and a higher bacterial mutation frequency in tCeD that contributes to higher interindividual variation at strain level. In addition, the immotile European subspecies of Eubacterium rectale, which has a distinct carbohydrate metabolism potential, was nearly absent in tCeD patients.

CONCLUSION: Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role in intestinal health and disease.},
}

Humans
*Celiac Disease/microbiology/diet therapy
*Gastrointestinal Microbiome/genetics
Male
Female
Feces/microbiology
Middle Aged
Adult
Netherlands
*Bacteria/classification/genetics/isolation & purification
Metagenomics
Aged

@article {pmid40289212,
year = {2025},
author = {Geertsema, J and Juncker, HG and Wilmes, L and Burchell, GL and de Rooij, SR and van Goudoever, JB and O'Riordan, KJ and Clarke, G and Cryan, JF and Korosi, A},
title = {Nutritional interventions to counteract the detrimental consequences of early-life stress.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40289212},
issn = {1476-5578},
abstract = {Exposure to stress during sensitive developmental periods comes with long term consequences for neurobehavioral outcomes and increases vulnerability to psychopathology later in life. While we have advanced our understanding of the mechanisms underlying the programming effects of early-life stress (ES), these are not yet fully understood and often hard to target, making the development of effective interventions challenging. In recent years, we and others have suggested that nutrition might be instrumental in modulating and possibly combatting the ES-induced increased risk to psychopathologies and neurobehavioral impairments. Nutritional strategies are very promising as they might be relatively safe, cheap and easy to implement. Here, we set out to comprehensively review the existing literature on nutritional interventions aimed at counteracting the effects of ES on neurobehavioral outcomes in preclinical and clinical settings. We identified eighty six rodent and ten human studies investigating a nutritional intervention to ameliorate ES-induced impairments. The human evidence to date, is too few and heterogeneous in terms of interventions, thus not allowing hard conclusions, however the preclinical studies, despite their heterogeneity in terms of designs, interventions used, and outcomes measured, showed nutritional interventions to be promising in combatting ES-induced impairments. Furthermore, we discuss the possible mechanisms involved in the beneficial effects of nutrition on the brain after ES, including neuroinflammation, oxidative stress, hypothalamus-pituitary-adrenal axis regulation and the microbiome-gut-brain axis. Lastly, we highlight the critical gaps in our current knowledge and make recommendations for future research to move the field forward.},
}

@article {pmid40289168,
year = {2025},
author = {Chancharoenthana, W and Kamolratanakul, S and Udompornpitak, K and Wannigama, DL and Schultz, MJ and Leelahavanichkul, A},
title = {Alcohol-induced gut permeability defect through dysbiosis and enterocytic mitochondrial interference causing pro-inflammatory macrophages in a dose dependent manner.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14710},
pmid = {40289168},
issn = {2045-2322},
mesh = {Animals ; *Dysbiosis/chemically induced/metabolism ; *Ethanol/toxicity/adverse effects ; Male ; *Mitochondria/drug effects/metabolism/pathology ; *Macrophages/drug effects/metabolism/pathology ; Permeability/drug effects ; Liver/drug effects/pathology/metabolism ; Oxidative Stress/drug effects ; Gastrointestinal Microbiome/drug effects ; Rats ; Apoptosis/drug effects ; Intestinal Mucosa/metabolism/drug effects ; Dose-Response Relationship, Drug ; },
abstract = {Although toxicity of alcohol toward the intestines and immunity is mentioned, there might be different effect of alcohol in a low and a high dose and the rodent model development using a simple SHIRPA binary score night be useful. Hence, a low and high dose of alcohol (6.30 and 1.26 g/kg/day) were administered in might for 16 weeks before determination of several parameters. As such, the peak blood alcohol concentration (BAC) of low and high dose of alcohol were approximately at 0.05 and 0.15%, respectively, at 1 h post-administration, which correlated with SHIRPA score at 1.8 ± 0.8 and 7.2 ± 0.6, respectively. After 16 wk of administration, a significant liver injury in high-dose alcohol was indicated by liver enzymes, liver weight, histology score, apoptosis, and hepatic accumulation of triglyceride (TG) and oxidative stress (malondialdehyde; MDA) with reduced anti-oxidant (glutathione). Meanwhile, low-dose alcohol demonstrated only elevated apoptosis with increased TG and MDA in liver tissue. Leaky gut from both dose of alcohol was also demonstrated by FITC-dextran, endotoxemia, serum beta glucan, and reduced occludin. However, bacterial abundance (microbiome analysis) of the feces from small bowel of high-dose alcohol, but not the low dose, was different from the control (increased Alitipes spp. with reduced Lachnospiraceae). In conclusion, both low- and high-dose alcohol induced leaky gut, while only the high-dose caused gut dysbiosis and alcohol damaged mitochondria but enhanced glycolysis in enterocytes and macrophages. Leaky gut might be more sensitive than dysbiosis to determine alcohol-induced intestinal injury.},
}

Animals
*Dysbiosis/chemically induced/metabolism
*Ethanol/toxicity/adverse effects
Male
*Mitochondria/drug effects/metabolism/pathology
*Macrophages/drug effects/metabolism/pathology
Permeability/drug effects
Liver/drug effects/pathology/metabolism
Oxidative Stress/drug effects
Gastrointestinal Microbiome/drug effects
Rats
Apoptosis/drug effects
Intestinal Mucosa/metabolism/drug effects
Dose-Response Relationship, Drug

@article {pmid40289138,
year = {2025},
author = {Weathers, SP and Li, X and Zhu, H and Damania, AV and Knafl, M and McKinley, B and Lin, H and Harrison, RA and Majd, NK and O'Brien, BJ and Penas-Prado, M and Loghin, M and Kamiya-Matsuoka, C and Yung, WKA and Solis Soto, LM and Maru, DM and Wistuba, I and Parra Cuentas, ER and Hernandez, S and Futreal, A and Wargo, JA and Schulze, K and Darbonne, WC and Ajami, NJ and Woodman, SE and de Groot, JF},
title = {Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a single arm prospective phase I/II trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3950},
pmid = {40289138},
issn = {2041-1723},
mesh = {Humans ; *Glioblastoma/genetics/immunology/mortality/therapy/drug therapy ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Female ; Middle Aged ; *Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy ; Temozolomide/therapeutic use/administration & dosage ; Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage ; Mutation ; Aged ; Adult ; *B7-H1 Antigen/antagonists & inhibitors ; Tumor Microenvironment ; Prospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use ; Treatment Outcome ; },
abstract = {This phase I/II trial aims to evaluate the efficacy of concurrent atezolizumab with radiation therapy and temozolomide (TMZ) followed by adjuvant atezolizumab and TMZ in newly diagnosed glioblastoma (GBM) patients and to identify pre-treatment correlates with outcome (N = 60). Trial number: NCT03174197. The primary outcome was overall survival (OS) whereas secondary outcomes were retrospective global-omics analyses to identify pre-treatment immune and genetic tumor features that correlated with survival. Concurrent use of atezolizumab with radiation and TMZ demonstrated OS in line with published trials for newly diagnosed GBM. Tumor genomic (WES and/or targeted NGS panel), transcriptomic (RNAseq) and tissue microenvironment imaging, as well as fecal metagenomic sequencing were conducted. Gene set enrichment analysis of tumors identified multiple immune-based transcriptomic programs to distinguish patients with longer versus shorter survival (p ≤ 0.01). GBM immune enrichment was highly associated with the pre-treatment tumor mesenchymal subtype and patient gastrointestinal bacterial taxa profile.},
}

Humans
*Glioblastoma/genetics/immunology/mortality/therapy/drug therapy
*Gastrointestinal Microbiome/genetics/drug effects
Male
Female
Middle Aged
*Brain Neoplasms/genetics/immunology/mortality/therapy/drug therapy
Temozolomide/therapeutic use/administration & dosage
Antibodies, Monoclonal, Humanized/therapeutic use/administration & dosage
Mutation
Aged
Adult
*B7-H1 Antigen/antagonists & inhibitors
Tumor Microenvironment
Prospective Studies
*Immune Checkpoint Inhibitors/therapeutic use
Treatment Outcome

@article {pmid40289103,
year = {2025},
author = {Fu, L and Baranova, A and Cao, H and Zhang, F},
title = {Gut microbiome links obesity to type 2 diabetes: insights from Mendelian randomization.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {253},
pmid = {40289103},
issn = {1471-2180},
mesh = {*Diabetes Mellitus, Type 2/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Mendelian Randomization Analysis ; *Obesity/microbiology/genetics/complications ; Body Mass Index ; Genome-Wide Association Study ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Research has established links between the gut microbiome (GM) and both obesity and type 2 diabetes (T2D), which is much discussed, but underexplored. This study employed body mass index (BMI) as the measurement of obesity to delve deeper into the correlations from a genetic perspective.

METHODS: We performed the Mendelian randomization (MR) analysis to examine the causal effects of GM on T2D and BMI, and vice versa. Genome-wide association study (GWAS) summary datasets were utilized for the analysis, including T2D (N = 933,970), BMI (N = 806,834), and two GM datasets from the international consortium MiBioGen (211 taxa, N = 18,340) and the Dutch Microbiome Project (DMP) (207 taxa, N = 7,738). These datasets mainly cover European populations, with additional cohorts from Asia and other regions. To further explore the potential mediating role of GM in the connections between BMI and T2D, their interaction patterns were summarized into a network.

RESULTS: MR analysis identified 9 taxa that showed protective properties against T2D. Seven species were within the Firmicutes and Bacteroidales phyla in the DMP, and two were from the MiBioGen (Odds Ratio (OR): 0.94-0.95). Conversely, genetic components contributing to the abundance of 12 taxa were associated with increased risks of T2D (OR: 1.04-1.12). Furthermore, T2D may elevate the abundance of seven taxa (OR: 1.03-1.08) and reduce the abundance of six taxa (OR: 0.93-0.97). In the analysis of the influence of the genetic component of BMI on GM composition, BMI affected 52 bacterial taxa, with 28 decreasing (OR: 0.75-0.92) and 24 increasing (OR: 1.08-1.27). Besides, abundances of 25 taxa were negatively correlated with BMI (OR: 0.95-0.99), while positive correlations were detected for 14 taxa (OR: 1.01-1.05). Notably, we uncovered 11 taxa genetically associated with both BMI and T2D, which formed an interactive network.

CONCLUSIONS: Our findings provide evidence for the GM-mediated links between obesity and T2D. The identification of relevant GM taxa offers valuable insights into the potential role of the microbiome in these diseases.},
}

*Diabetes Mellitus, Type 2/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Humans
*Mendelian Randomization Analysis
*Obesity/microbiology/genetics/complications
Body Mass Index
Genome-Wide Association Study
*Bacteria/classification/genetics/isolation & purification

@article {pmid40288428,
year = {2025},
author = {Wang, W and Chen, Y and Rasic, M and Ascoli, C and Hatch, JE and Nemsick, NK and Deschamp, AR and Davis, SD and Sanders, DB and Ranganathan, S and Stick, S and Perkins, DL and Thomas Ferkol, and Finn, PW},
title = {An Observational Study of the Lung Microbiome and Lung Function in Young Children with Cystic Fibrosis Across Two Countries with Differing Antibiotic Practices.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107628},
doi = {10.1016/j.micpath.2025.107628},
pmid = {40288428},
issn = {1096-1208},
abstract = {BACKGROUND: Cystic fibrosis (CF) lung disease begins early, and prophylactic antibiotics have been used to prevent Staphylococcus aureus infection. This study examined the lung microbiome in two countries with differing antibiotic practices and its relationship to lung function in young children with CF.

METHODS: A binational, longitudinal, observational study was performed to define the lower airway microbiome in infants with CF. 16S rRNA sequencing was performed using lavage fluid to characterize the lung microbiota in 45 infants with and without prophylactic antibiotic therapy at an average age of approximately 3 months and 14 months. The association between pulmonary function, bacterial community diversities, and taxa was assessed.

RESULTS: Expected CF bacterial genera and non-traditional bacteria, such as Streptococcus, were identified as core taxa. Microbial community shifts were observed in infants who received antibiotic prophylaxis, with lower alpha diversity (ANOVA, P<0.05) and a higher proportion of Streptococcus at the first visit. Beta diversity (FEV0.5z; MiRKAT, P<0.05) and Streptococcus were associated with FEV0.5z (LASSO and linear regression, β<0). Functional annotation suggested that alteration of lung microbiota may be linked to antimicrobial resistance.

CONCLUSIONS: Lung microbial diversity in infants with CF varied between the two countries, particularly during early infancy. A shift in the lung microbiome toward a higher relative abundance of Streptococcus was associated with reduced pulmonary function.},
}

@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.},
}