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

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

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

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

@article {pmid40371708,
year = {2025},
author = {Attaye, I and Bird, JK and Nieuwdorp, M and Gül, S and Seegers, JFML and Morrison, S and Hofkens, S and Herrema, H and Bui, N and Puhlmann, ML and de Vos, WM},
title = {Anaerobutyricum soehngenii improves glycemic control and other markers of cardio-metabolic health in adults at risk of type 2 diabetes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2504115},
doi = {10.1080/19490976.2025.2504115},
pmid = {40371708},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism/microbiology/prevention & control ; Middle Aged ; Male ; Female ; Double-Blind Method ; *Glycemic Control ; Adult ; Glycated Hemoglobin/analysis/metabolism ; Blood Glucose/metabolism ; Aged ; Prediabetic State/therapy ; Biomarkers/blood ; Blood Pressure ; Gastrointestinal Microbiome ; Europe ; },
abstract = {Anaerobutyricum soehngenii (previously Eubacterium hallii) is a butyrate-producing next-generation beneficial microbe generally recognized as safe. Several short-term intervention trials by A. soehngenii L2-7 have shown improvement of insulin sensitivity in prediabetic subjects and type 2 diabetes patients. To determine the long-term cardiometabolic benefits and safety, we performed a 3-month double-blind, randomized placebo-controlled intervention in 98 prediabetic insulin-resistant adults in Europe and U.S. with daily administration of encapsulated cells of A. soehngenii CH-106, a tetracycline-sensitive isogenic derivative of strain L2-7. Compared to placebo, A. soehngenii-treated subjects showed significantly reduced glycemic variability (1% reduction in the coefficient of variation; p = 0.01) and improved glycemic control (6% reduction in the overall net glycemic action-1; p < 0.05), including reduced serum glycated hemoglobin (HbA1c) levels when including the 4-week washout period (1 mmol/mol reduction; p < 0.05). Moreover, diastolic blood pressure was significantly reduced in all A. soehngenii-treated subjects (3 mm Hg; p < 0.05). The study product was well-tolerated and had no effect on the global intestinal microbiota composition, including alpha and beta-diversity, besides an increased abundance of A. soehngenii in the treatment group, indicative of compliance. The U.S. participants, compared to those in Europe, responded best, notably in the oral glucose tolerance tests (15% improvement in the area-under-the curve of plasma glucose levels; p = 0.039) or coefficient of variation (reduction of 3.1%; p < 0.05). This potentially relates to a more severe prediabetic state in U.S. subjects, associated with significantly reduced (1.5-3.5-fold) relative abundance of Bifidobacterium, Coprococcus, Ruminococcus spp. and two-fold increased relative abundance of Lachnoclostridium spp. In conclusion, daily oral supplementation with A. soehngenii was safe and improved various markers of glycemic control, reduced HbA1c levels and diastolic blood pressure, indicating a novel microbiome-based approach to improve cardio-metabolic health in adults at risk for developing type 2 diabetes.Clinical trial reg. no. NCT04529473, clinicaltrials.govSocial media summary 120 characters: Anaerobutyricum soehngenii supplementation improves #cardio-metabolic health in subjects at risk for type 2 #diabetes.},
}

Humans
*Diabetes Mellitus, Type 2/metabolism/microbiology/prevention & control
Middle Aged
Male
Female
Double-Blind Method
*Glycemic Control
Adult
Glycated Hemoglobin/analysis/metabolism
Blood Glucose/metabolism
Aged
Prediabetic State/therapy
Biomarkers/blood
Blood Pressure
Gastrointestinal Microbiome
Europe

@article {pmid40371158,
year = {2025},
author = {Liu, Y and Ning, H and Li, Y and Li, Y and Ma, J},
title = {The microbiota in breast cancer: dysbiosis, microbial metabolites, and therapeutic implications.},
journal = {American journal of cancer research},
volume = {15},
number = {4},
pages = {1384-1409},
pmid = {40371158},
issn = {2156-6976},
abstract = {The human microbiome plays a pivotal role in host health and disease, with emerging evidence underscoring its significant influence on the development and progression of breast cancer. Studies have revealed that dysbiosis in both the gut and breast tissue microbiota is strongly associated with an elevated risk of breast cancer. Distinct microbial profiles have been identified among healthy individuals, patients with benign breast conditions, and those with malignant tumors, with further variations observed across different ethnic groups and breast cancer subtypes. The complex interplay between breast cancer risk factors and microbial populations, coupled with the direct impact of microbial communities and their metabolites on inflammatory pathways and immune responses, underscores the importance of this field. Additionally, the interaction between gut microbiota and therapeutic modalities such as chemotherapy and radiotherapy is of particular interest, as these interactions can significantly influence treatment outcomes, either enhancing or diminishing efficacy. This review explores the effects of the Mediterranean diet, probiotics, prebiotics, and natural medicinal products on gut microbiota, emphasizing their potential as innovative therapeutic strategies. Notably, the use of engineered probiotics within the tumor microenvironment represents a promising frontier in breast cancer treatment. In conclusion, research on the human microbiome not only deepens our understanding of breast cancer pathogenesis but also lays the groundwork for the development of novel and targeted therapeutic interventions.},
}

@article {pmid40370098,
year = {2025},
author = {Wang, N and Wu, M and Gu, W and Dai, C and Shao, Z and Subbalakshmi, KP},
title = {MSFT-transformer: a multistage fusion tabular transformer for disease prediction using metagenomic data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf217},
pmid = {40370098},
issn = {1477-4054},
support = {JUSRP123035//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Computational Biology/methods ; Algorithms ; },
abstract = {More and more recent studies highlight the crucial role of the human microbiome in maintaining health, while modern advancements in metagenomic sequencing technologies have been accumulating data that are associated with human diseases. Although metagenomic data offer rich, multifaceted information, including taxonomic and functional abundance profiles, their full potential remains underutilized, as most approaches rely only on one type of information to discover and understand their related correlations with respect to disease occurrences. To address this limitation, we propose a multistage fusion tabular transformer architecture (MSFT-Transformer), aiming to effectively integrate various types of high-dimensional tabular information extracted from metagenomic data. Its multistage fusion strategy consists of three modules: a fusion-aware feature extraction module in the early stage to improve the extracted information from inputs, an alignment-enhanced fusion module in the mid stage to enforce the retainment of desired information in cross-modal learning, and an integrated feature decision layer in the late stage to incorporate desired cross-modal information. We conduct extensive experiments to evaluate the performance of MSFT-Transformer over state-of-the-art models on five standard datasets. Our results indicate that MSFT-Transformer provides stable performance gains with reduced computational costs. An ablation study illustrates the contributions of all three models compared with a reference multistage fusion transformer without these novel strategies. The result analysis implies the significant potential of the proposed model in future disease prediction with metagenomic data.},
}

*Metagenomics/methods
Humans
*Metagenome
*Computational Biology/methods
Algorithms

@article {pmid40369669,
year = {2025},
author = {Purse, C and Parker, A and James, SA and Baker, DJ and Moss, CJ and Evans, R and Durham, J and Funnell, SGP and Carding, SR},
title = {Intestinal microbiota profiles of captive-bred cynomolgus macaques reveal influence of biogeography and age.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {47},
pmid = {40369669},
issn = {2524-4671},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1//BBSRC/ ; },
abstract = {BACKGROUND: Age-associated changes to the intestinal microbiome may be linked to inflammageing and the development of age-related chronic diseases. Cynomolgus macaques, a common animal model in biomedical research, have strong genetic physiological similarities to humans and may serve as beneficial models for the effect of age on the human microbiome. However, age-associated changes to their intestinal microbiome have previously only been investigated in faecal samples. Here, we have characterised and investigated the effects of age in the cynomolgus macaque intestinal tract in luminal samples from both the small and large intestine.

RESULTS: Whole metagenomic shotgun sequencing was used to analyse the microbial communities in intestinal content obtained from six different intestinal regions, covering the duodenum to distal colon, of 24 healthy, captive-bred cynomolgus macaques, ranging in age from 4 to 20 years. Both reference-based and assembly-based computational profiling approaches were used to analyse changes to intestinal microbiota composition and metabolic potential associated with intestinal biogeography and age. Reference-based computational profiling revealed a significant and progressive increase in both species richness and evenness along the intestinal tract. The microbial community composition also significantly differed between the small intestine, caecum, and colon. Notably, no significant changes in the taxonomic abundance of individual taxa with age were found except when sex was included as a covariate. Additionally, using an assembly-based computational profiling approach, 156 putative novel bacterial and archaeal species were identified.

CONCLUSIONS: We observed limited effects of age on the composition of the luminal microbiota in the profiled regions of the intestinal tract except when sex was included as a covariate. The enteric microbial communities of the small and the large intestine were, however, distinct, highlighting the limitations of frequently used faecal microbial profiling as a proxy for the intestinal microbiota. The identification of a number of putative novel microbial taxa contributes to knowledge of the full diversity of the cynomolgus macaque intestinal microbiome.},
}

@article {pmid40369630,
year = {2025},
author = {Dong, R and Li, M and Gu, XF and Gao, H and Wei, Z and Qi, H and Zhang, J and Feng, Q},
title = {The surface protein Gbp of Fusobacterium nucleatum inhibits osteogenic differentiation by inactivating the Wnt/β-catenin pathway via binding to Annexin A2.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {540},
pmid = {40369630},
issn = {1479-5876},
support = {82270980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; the National Clinical Key Specialty (Periodontology) Construction Project//the National Clinical Key Specialty (Periodontology) Construction Project/ ; the National Young Scientist Support Foundation (2019)//the National Young Scientist Support Foundation (2019)/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; },
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease that significantly impacts periodontal bone regeneration, yet the distinct biological features of osteoblasts in this condition remain poorly understood. This study aims to elucidate the cellular and molecular mechanisms underlying osteoblast dysfunction in periodontitis, with a focus on the role of Fusobacterium nucleatum (Fn) and its effector protein, D-galactose-binding periplasmic protein (Gbp).

METHOD: Single-cell RNA sequencing (scRNA-seq) data from human gingival tissues of periodontitis patients (PD) and healthy controls (HC) were analyzed to identify cellular heterogeneity and molecular pathways. An experimental periodontitis model in mice and primary osteoblast cultures were used to investigate the effects of Fn and Gbp on osteogenic differentiation. Transcriptomic analysis, gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) networks were employed to explore the underlying mechanisms.

RESULTS: scRNA-seq revealed a reduction in mesenchymal stem cells (MSCs) and osteoblastic lineage cells in PD tissues, with significant downregulation of osteogenic pathways such as Wnt signaling. Fn infection induced alveolar bone destruction in vivo and inhibited osteoblast proliferation, differentiation, and mineralization in vitro. Gbp, an Fn adhesin, similarly impaired osteogenic differentiation by downregulating key osteogenic genes and pathways. Transcriptomic analysis identified shared inflammatory and osteogenic pathways affected by Fn and Gbp, with NF-κB signaling activated and Wnt/β-catenin signaling inhibited. Mechanistically, Gbp interacted with the host protein ANXA2, disrupting the ANXA2/GSK3β complex and inhibiting Wnt/β-catenin signaling, a pivotal route for osteoblast differentiation. ANXA2 knockdown mitigated the Fn/Gbp-induced suppression of osteogenic activity, emphasizing its role in Fn-induced bone loss.

CONCLUSION: This study demonstrates that Fn and its effector Gbp disrupt osteogenic differentiation by inactivating the Wnt/β-catenin pathway binding to ANXA2.},
}

@article {pmid40363959,
year = {2025},
author = {Gullo, G and Satullo, M and Billone, V and De Paola, L and Petousis, S and Kotlik, Y and Margioula-Siarkou, C and Perino, A and Cucinella, G},
title = {The Role of the Genital Tract Microbiome in Human Fertility: A Literature Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/jcm14092923},
pmid = {40363959},
issn = {2077-0383},
abstract = {Background/Objectives: Infertility is a multifactorial condition influenced by various factors, including dysbiosis and alterations in the genital tract microbiome. Recent studies emphasize the microbiome's significant role in influencing a woman's fertility potential, thereby affecting the chances of spontaneous conception and the outcomes of assisted reproductive treatments. Understanding the microbial characteristics and unique features of a healthy genital microbiome, as well as how changes in its composition can impact fertility, would allow for a more comprehensive and personalized approach to managing assisted reproductive treatments. The microbiome also influences pregnancy outcomes, and restoring its balance has been shown to improve fertility in infertile couples. The human microbiome plays a key role in maintaining the body's overall health. Disruptions in microbiome balance among women of reproductive age can contribute to a range of pregnancy-related complications, with notable consequences for both maternal and fetal well-being. Emerging research has highlighted a connection between the reproductive tract microbiome and outcomes of assisted reproductive technologies (ART), suggesting that re-establishing a healthy microbial environment may enhance fertility in couples facing infertility. Methods: We conducted a search on PubMed using the keywords "microbiome", "infertility", and "ART" over the past 10 years. This article aims to provide an updated overview of the role of the microbiome in female reproductive health, with a focus on its implications for fertility treatment. Results: The microbiome has a significant role in influencing women's fertility. Conclusions: Understanding the microbiome's impact on fertility and pregnancy outcomes may lead to more effective and personalized approaches in fertility treatments, improving the chances of successful conception and pregnancy.},
}

@article {pmid40362812,
year = {2025},
author = {Cominelli, G and Sulas, F and Pinto, D and Rinaldi, F and Favero, G and Rezzani, R},
title = {Neuro-Nutritional Approach to Neuropathic Pain Management: A Critical Review.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091502},
pmid = {40362812},
issn = {2072-6643},
support = {Grant donation//Franchini Acciai S.p.A./ ; },
mesh = {Humans ; *Neuralgia/diet therapy/therapy ; *Melatonin/administration & dosage/therapeutic use ; Antioxidants/administration & dosage ; *Pain Management/methods ; Dietary Supplements ; Quality of Life ; *Diet ; Oxidative Stress ; },
abstract = {Pain is a significant global public health issue that can interfere with daily activities, sleep, and interpersonal relationships when it becomes chronic or worsens, ultimately impairing quality of life. Despite ongoing efforts, the efficacy of pain treatments in improving outcomes for patients remains limited. At present, the challenge lies in developing a personalized care and management plan that helps to maintain patient activity levels and effectively manages pain. Neuropathic pain is a chronic condition resulting from damage to the somatosensory nervous system, significantly impacting quality of life. It is partly thought to be caused by inflammation and oxidative stress, and clinical research has suggested a link between this condition and diet. However, these links are not yet well understood and require further investigation to evaluate the pathways involved in neuropathic pain. Specifically, the question remains whether supplementation with dietary antioxidants, such as melatonin, could serve as a potential adjunctive treatment for neuropathic pain modulation. Melatonin, primarily secreted by the pineal gland but also produced by other systems such as the digestive system, is known for its anti-inflammatory, antioxidant, and anti-aging properties. It is found in various fruits and vegetables, and its presence alongside other polyphenols in these foods may enhance melatonin intake and contribute to improved health. The aim of this review is to provide an overview of neuropathic pain and examine the potential role of melatonin as an adjunctive treatment in a neuro-nutritional approach to pain management.},
}

Humans
*Neuralgia/diet therapy/therapy
*Melatonin/administration & dosage/therapeutic use
Antioxidants/administration & dosage
*Pain Management/methods
Dietary Supplements
Quality of Life
*Diet
Oxidative Stress

@article {pmid40362760,
year = {2025},
author = {Sechi, A and Cedirian, S and Brunetti, T and Quadrelli, F and Torres, F and Tosti, A and Rinaldi, F and Pinto, D and Bolognino, R and Marzano, AV and Piraccini, BM},
title = {Safety First: A Comprehensive Review of Nutritional Supplements for Hair Loss in Breast Cancer Patients.},
journal = {Nutrients},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/nu17091451},
pmid = {40362760},
issn = {2072-6643},
mesh = {Humans ; *Dietary Supplements/adverse effects ; *Breast Neoplasms/therapy/drug therapy/complications ; Female ; *Alopecia/etiology/chemically induced/drug therapy/prevention & control ; Antioxidants/adverse effects/administration & dosage ; Quality of Life ; Vitamin D/adverse effects/administration & dosage ; },
abstract = {Among the distressing side effects of cancer treatments, hair loss is one of the most disturbing for the quality of life and adherence to therapy in breast cancer patients. Many patients take nutritional supplements to prevent hair loss or enhance regrowth. Based on their mechanism and timing of use, nutritional supplements could be divided into safe, cautious, debated, and contraindicated categories. Non-contraindicated supplements generally include safe supplements like vitamin D, which is not known to interfere with cancer treatments. Those that are contraindicated include phytoestrogens and compounds affecting estrogen pathways because of the risk of stimulating tumor growth in cancers sensitive to estrogen. Antioxidants like tocotrienols and resveratrol are given judiciously because of potential interference with cancer therapies dependent on reactive oxygen species. Supplements debated, including nicotinamide, folate, and iron, pose a risk by promoting cellular proliferation or altering the tumor microenvironment. Biotin is nontoxic but interferes with blood test results and is thus difficult in cancer monitoring. Evidence regarding nutritional supplements' safety and efficacy in this context is conflicting. Management by an oncologist is required along with more studies to clearly establish the safety parameters and efficacy guidelines.},
}

Humans
*Dietary Supplements/adverse effects
*Breast Neoplasms/therapy/drug therapy/complications
Female
*Alopecia/etiology/chemically induced/drug therapy/prevention & control
Antioxidants/adverse effects/administration & dosage
Quality of Life
Vitamin D/adverse effects/administration & dosage

@article {pmid40359847,
year = {2025},
author = {Liu, S and Ao, C and Li, Z and Chio, LH and Gu, Y and Zhan, H and Li, H and Li, H and Li, Z and Wang, Q},
title = {Development and validation of a polysomnography-based nomogram for predicting amnestic mild cognitive impairment in middle-aged and elderly people.},
journal = {Sleep medicine},
volume = {132},
number = {},
pages = {106564},
doi = {10.1016/j.sleep.2025.106564},
pmid = {40359847},
issn = {1878-5506},
abstract = {BACKGROUND: Amnestic mild cognitive impairment (aMCI) is a subtype of mild cognitive impairment (MCI) that is considered an early stage of Alzheimer's disease (AD). Although early identification of aMCI is crucial for mitigating disease progression, objective and economic evaluation tools designed for aMCI prediction are lacking. Hence, we aimed to develop and validate a novel nomogram based on sleep characteristics to predict the risk of aMCI in middle-aged and elderly adults.

METHODS: This study included 817 eligible participants who underwent polysomnography (PSG), comprising 339 individuals diagnosed with aMCI. The participants were divided into a training cohort and a validation cohort using a 7:3 random split. Least absolute shrinkage and selection operator (LASSO) regression was employed to identify key predictive factors, followed by multivariable logistic regression to refine the predictors, which were subsequently used to construct a nomogram. The predictive performance of the nomogram was evaluated through receiver operating characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA).

RESULTS: Among the 30 potential predictors, 9 independent sleep-related predictors were incorporated into the final nomogram: total sleep time (TST), sleep efficiency (SE), the proportions of nonrapid eye movement stage 1 (N1), nonrapid eye movement stage 3 (N3), and rapid eye movement (REM) sleep, the density and amplitude of fast spindles and the density and amplitude of K-complexes (KCs). The nomogram demonstrated excellent discriminative ability, with an area under the curve (AUC) of 0.968 in the training cohort and 0.953 in the validation cohort. Calibration curves indicated strong agreement between the predicted and observed outcomes, and DCA confirmed the clinical usefulness of the nomogram by showing consistent net benefits across a wide range of threshold probabilities.

CONCLUSION: In this study, we developed and validated an innovative nomogram based on objective sleep characteristics to predict aMCI risk. By reducing the reliance on subjective or costly diagnostic tools, the nomogram offers a reliable, accessible, and practical method for the early identification of aMCI.},
}

@article {pmid40335149,
year = {2025},
author = {Koskenvuo, L and Paajanen, P and Varpe, P and Seppälä, T and Mentula, P and Haapamäki, C and Carpelan-Holmström, M and Carpelan, A and Lehto, K and Satokari, R and Lepistö, A and Sallinen, V},
title = {PROtective ileoStomy versus ProtectivE colostomy in anterior Rectal resectIon: study protocol for a multicenter, open-label, randomised conTrolled studY (PROSPERITY).},
journal = {BMJ open},
volume = {15},
number = {5},
pages = {e096091},
doi = {10.1136/bmjopen-2024-096091},
pmid = {40335149},
issn = {2044-6055},
abstract = {INTRODUCTION: Loop ileostomy and loop colostomy are both used to form a protective stoma after anterior resection. Evidence regarding which of these two procedures is superior is lacking. Furthermore, no studies comparing changes in the microbiome after loop ileostomy or loop colostomy exist.

METHODS AND ANALYSIS: This multicentre, open-label, superiority, individually randomised controlled trial will include patients who undergo anterior rectal resection with primary anastomosis with a protective stoma. The exclusion criteria are patients who already have a stoma, technical inability to create either type of stoma, aged <18 years and inadequate cooperation. Patients scheduled for anterior rectal resection will be randomised intraoperatively in a 1:1 ratio to undergo either loop ileostomy or loop colostomy. The primary outcome is cumulative stoma-related adverse events within 60 days after primary surgery, measured using the Comprehensive Complication Index (CCI). Secondary outcomes include all postoperative complications (measured using the CCI), number of hospital-free days within 30 days after primary surgery, quality of life at 2 months (measured using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaires-Core 30 and Colorectal 29), complications within 30 days after stoma closure (measured using the CCI) and kidney function (measured using estimated glomerular filtration rate) at 1 year. Tertiary outcomes are survival, kidney function and number of stoma site hernias at 5 years. The sample size was calculated to detect a mean difference of five CCI points between groups, resulting in a final sample size of 350 patients. Microbiome samples will be collected from the faeces and mucous membrane from patients in Helsinki University Hospital.

ETHICS AND DISSEMINATION: The Ethics Committee of Helsinki University Hospital approved the study (approval number 4579/2024). The findings will be disseminated in peer-reviewed academic journals.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT06650085, registered on 20 August 2024.

PROTOCOL VERSION: Version 3.0, dated 17 April 2025.},
}

@article {pmid40333113,
year = {2025},
author = {Bordea, MA and Nutz, BTG and Chiorean, AD and Samasca, G and Lupan, I and Simon, LM and Pepelea, L},
title = {Microbial Interactions in Nature: The Impact of Gram-Negative Bacilli on the Hyphal Growth of Candida albicans.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040327},
pmid = {40333113},
issn = {2076-0817},
mesh = {*Candida albicans/growth & development/pathogenicity ; Humans ; *Microbial Interactions ; *Hyphae/growth & development ; *Gram-Negative Bacteria/physiology ; Coinfection/microbiology ; *Candidiasis/microbiology ; Virulence ; Microbiota ; },
abstract = {The escalating global prevalence of fungal and bacterial co-infections underscores the significant and multifaceted impact of ubiquitous microorganisms on both environmental equilibria and human well-being. The human microbiome, a complex ecosystem of bacterial communities, harbors opportunistic pathogens capable of inducing superinfections or concurrent infections with Candida spp. The intricate interplay, exemplified by the interaction between Candida albicans and diverse bacteria, necessitates rigorous investigation to elucidate mechanisms by which this polymicrobial behavior potentiates fungal virulence, particularly in immunocompromised individuals. Our study aims to comprehensively examine the ramifications of these interactions, with a specific focus on their influence on fungal virulence and the consequent exacerbation of disease severity. Achieving a comprehensive understanding of these complex relationships is paramount for informing effective clinical management strategies for infectious diseases, and the accurate identification of fungal-bacterial co-infections holds substantial implications for optimizing clinical treatment paradigms, especially in vulnerable immunocompromised hosts.},
}

*Candida albicans/growth & development/pathogenicity
Humans
*Microbial Interactions
*Hyphae/growth & development
*Gram-Negative Bacteria/physiology
Coinfection/microbiology
*Candidiasis/microbiology
Virulence
Microbiota

@article {pmid40330025,
year = {2025},
author = {Smail, SW and Albarzinji, N and Salih, RH and Taha, KO and Hirmiz, SM and Ismael, HM and Noori, MF and Azeez, SS and Janson, C},
title = {Microbiome dysbiosis in SARS-CoV-2 infection: implication for pathophysiology and management strategies of COVID-19.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1537456},
pmid = {40330025},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/microbiology/therapy ; *COVID-19/microbiology/physiopathology/therapy/complications ; *SARS-CoV-2 ; *Gastrointestinal Microbiome ; },
abstract = {The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), in late 2019 initiated a global health crisis marked by widespread infection, significant mortality, and long-term health implications. While SARS-CoV-2 primarily targets the respiratory system, recent findings indicate that it also significantly disrupts the human microbiome, particularly the gut microbiota, contributing to disease severity, systemic inflammation, immune dysregulation, and increased susceptibility to secondary infections and chronic conditions. Dysbiosis, or microbial imbalance, exacerbates the clinical outcomes of COVID-19 and has been linked to long-COVID, a condition affecting a significant proportion of survivors and manifesting with over 200 symptoms across multiple organ systems. Despite the growing recognition of microbiome alterations in COVID-19, the precise mechanisms by which SARS-CoV-2 interacts with the microbiome and influences disease progression remain poorly understood. This narrative review investigates the impact of SARS-CoV-2 on host-microbiota dynamics and evaluates its implications in disease severity and for developing personalized therapeutic strategies for COVID-19. Furthermore, it highlights the dual role of the microbiome in modulating disease progression, and as a promising target for advancing diagnostic, prognostic, and therapeutic approaches in managing COVID-19.},
}

Humans
*Dysbiosis/microbiology/therapy
*COVID-19/microbiology/physiopathology/therapy/complications
*SARS-CoV-2
*Gastrointestinal Microbiome

@article {pmid40329426,
year = {2025},
author = {Ren, L and Yang, J and Xiao, Y and Guo, L and Rao, J and Wu, C and Wang, X and Wang, Y and Zhang, L and Zhang, L and Jiang, X and Zhong, J and Zhong, J and Yang, W and Wang, C and Wang, J and Li, M},
title = {Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {115},
pmid = {40329426},
issn = {2049-2618},
support = {2020-I2M-2-013//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2023-I2M-2-001//Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS)/ ; 2019PT310029//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; NSFC82221004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS: We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS: In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.},
}

@article {pmid40328944,
year = {2025},
author = {Kim, Y and Worby, CJ and Acharya, S and van Dijk, LR and Alfonsetti, D and Gromko, Z and Azimzadeh, PN and Dodson, KW and Gerber, GK and Hultgren, SJ and Earl, AM and Berger, B and Gibson, TE},
title = {Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1184-1197},
pmid = {40328944},
issn = {2058-5276},
support = {R35GM143056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21AI154075//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149270//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK121822//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U19AI110818//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM141861//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The ability to detect and quantify microbiota over time from shotgun metagenomic data has a plethora of clinical, basic science and public health applications. Given these applications, and the observation that pathogens and other taxa of interest can reside at low relative abundance, there is a critical need for algorithms that accurately profile low-abundance microbial taxa with strain-level resolution. Here we present ChronoStrain: a sequence quality- and time-aware Bayesian model for profiling strains in longitudinal samples. ChronoStrain explicitly models the presence or absence of each strain and produces a probability distribution over abundance trajectories for each strain. Using synthetic and semi-synthetic data, we demonstrate how ChronoStrain outperforms existing methods in abundance estimation and presence/absence prediction. Applying ChronoStrain to two human microbiome datasets demonstrated its improved interpretability for profiling Escherichia coli strain blooms in longitudinal faecal samples from adult women with recurring urinary tract infections, and its improved accuracy for detecting Enterococcus faecalis strains in infant faecal samples. Compared with state-of-the-art methods, ChronoStrain's ability to detect low-abundance taxa is particularly stark.},
}

@article {pmid40322904,
year = {2025},
author = {Hinkkanen, VI and Savinko, T and Palosuo, K and Alenius, H and Mäkelä, MJ and Karisola, P},
title = {Regular Allergen Exposure During Oral Immunotherapy Alters the Transcriptomic Innate Immune Response After Cellular Restimulation in Children With Egg Allergy.},
journal = {Journal of investigational allergology & clinical immunology},
volume = {},
number = {},
pages = {0},
doi = {10.18176/jiaci.1079},
pmid = {40322904},
issn = {1018-9068},
abstract = {BACKGROUND AND OBJECTIVES: Oral immunotherapy (OIT) is a promising treatment for food allergies. However, the molecular mechanisms leading to desensitization remain unknown. To better understand the immunological mechanisms and transcriptional changes underlying desensitization to food allergens during OIT.

METHODS: Our cohort consisted of 40 Finnish children with egg allergy who underwent OIT. Peripheral blood mononuclear cells (PBMCs) were collected at 0, 3, and 8 months of therapy and stimulated with an egg allergen extract. Differentially expressed genes (DEGs) were identified based on quantile-normalized and batch-corrected microarray data using a linear model. Gene enrichment and Pearson correlation analyses were conducted.

RESULTS: After 8 months of therapy, 45% of patients were fully desensitized and 55% partially desensitized. Stimulation with egg yielded 49 DEGs at 0 months, 723 DEGs at 3 months, and 759 DEGs at 8 months in PBMCs after comparison with unstimulated controls. At 8 months of OIT, allergen stimulation led to down regulation of proinflammatory pathways, as well as IL-4 and IL-13 signaling. At baseline, the immune response in the fully desensitized group was more reactive than in the partially desensitized group.

CONCLUSIONS: During OIT, general immune activity is increased, especially the number of down-regulated genes, suggesting active immune suppression. Transcriptomic profiles differ between fully and partially desensitized patients, with a notably more reactive immune response in the fully desensitized group at baseline. Innate immunity seems to play a significant role in the development of desensitization during OIT.},
}

@article {pmid40322851,
year = {2025},
author = {Zeng, Z and Li, M and Vannucci, M},
title = {Bayesian covariate-dependent graph learning with a dual group spike-and-slab prior.},
journal = {Biometrics},
volume = {81},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujaf053},
pmid = {40322851},
issn = {1541-0420},
support = {2153704//DMS/NIGMS/ ; //National Science Foundation/ ; },
mesh = {Bayes Theorem ; Computer Simulation ; Humans ; *Models, Statistical ; Microbiota ; Algorithms ; },
abstract = {Covariate-dependent graph learning has gained increasing interest in the graphical modeling literature for the analysis of heterogeneous data. This task, however, poses challenges to modeling, computational efficiency, and interpretability. The parameter of interest can be naturally represented as a 3-dimensional array with elements that can be grouped according to 2 directions, corresponding to node level and covariate level, respectively. In this article, we propose a novel dual group spike-and-slab prior that enables multi-level selection at covariate-level and node-level, as well as individual (local) level sparsity. We introduce a nested strategy with specific choices to address distinct challenges posed by the various grouping directions. For posterior inference, we develop a full Gibbs sampler for all parameters, which mitigates the difficulties of parameter tuning often encountered in high-dimensional graphical models and facilitates routine implementation. Through simulation studies, we demonstrate that the proposed model outperforms existing methods in its accuracy of graph recovery. We show the practical utility of our model via an application to microbiome data where we seek to better understand the interactions among microbes as well as how these are affected by relevant covariates.},
}

Bayes Theorem
Computer Simulation
Humans
*Models, Statistical
Microbiota
Algorithms

@article {pmid40315414,
year = {2025},
author = {Galperina, A and Lugli, GA and Milani, C and De Vos, WM and Ventura, M and Salonen, A and Hurwitz, B and Ponsero, AJ},
title = {The Aggregated Gut Viral Catalogue (AVrC): A unified resource for exploring the viral diversity of the human gut.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1012268},
doi = {10.1371/journal.pcbi.1012268},
pmid = {40315414},
issn = {1553-7358},
abstract = {The growing interest in the role of the gut virome in human health and disease, has led to several recent large-scale viral catalogue projects mining human gut metagenomes each using varied computational tools and quality control criteria. Importantly, there has been to date no consistent comparison of these catalogues' quality, diversity, and overlap. In this project, we therefore systematically surveyed nine previously published human gut viral catalogues. While these catalogues collectively screened >40,000 human fecal metagenomes, 82% of the recovered 345,613 viral sequences were unique to one catalogue, highlighting limited redundancy between the ressources and suggesting the need for an aggregated resource bringing these viral sequences together. We further expanded these viral catalogues by mining 7,867 infant gut metagenomes from 12 large-scale infant studies collected in 9 different countries. From these datasets, we constructed the Aggregated Gut Viral Catalogue (AVrC), a unified modular resource containing 1,018,941 dereplicated viral sequences (449,859 species-level vOTUs). Using computational inference tools, annotations were obtained for each vOTU representative sequence quality, viral taxonomy, predicted viral lifestyle, and putative host. This project aims to facilitate the reuse of previously published viral catalogues by the research community and follows a modular framework to enable future expansions as novel data becomes available.},
}

@article {pmid40314735,
year = {2025},
author = {Rohde, C},
title = {[Basic knowledge of phages and their therapeutic application].},
journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz},
volume = {},
number = {},
pages = {},
pmid = {40314735},
issn = {1437-1588},
abstract = {Phages (bacteriophages) are viruses that specifically infect and kill bacteria. They are very abundant in nature, playing a highly relevant role in microbial ecosystems. In medicine, they are investigated as a potential alternative or supplement to antibiotics and can be used to treat wound, urinary tract and lung infections, for example. Single phages or so-called "phage cocktails" are applied.This overview article on basic knowledge of phages sheds light on well-known keywords from classical knowledge of phage biology and on state-of-the-art research focuses. Mechanisms of phage activity are presented as a basis for therapeutic application. Particularly, the phage-host interaction, lysis mechanisms, phage morphologies and specific methods for visualisation are discussed. Being part of the human microbiome, phages contribute to immune defence, especially in the mucosa. Temperate phages that are able to reside in bacterial genomes as prophages and therefore not suitable for therapy use as well as the CrAss phages (Crassvirales) and Lak megaphages discovered in recent years are also introduced. Further topics are bacterial phage defence, phage resistance and phage-antibiotic synergies. An outlook on future research is given, emphasising the importance of a coordinated collection of scientific results.Phages should not replace antibiotics, but they can even improve their efficiency. Currently, the licensing processes for phage therapy are still challenging. However, trust in phage preparations must be based on quality, which has to be guaranteed by harmonised standards.},
}

@article {pmid40314614,
year = {2025},
author = {Lee, WM and Ahn, SY and Lee, GS and Park, I and Kim, J and Lee, SH and Lee, S and Kim, CS},
title = {Discovery and Biosynthesis of Indole-Functionalized Metabolites from the Human Blood Bacterium, Paracoccus sanguinis, and Their Anti-Skin Aging Activity.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.4c01354},
pmid = {40314614},
issn = {1520-6025},
abstract = {The human microbiome plays a crucial role in health and disease, with microbial metabolites acting as key mediators of physiological processes. While extensive research has focused on gut-derived microbes, the metabolic contributions of blood-derived bacteria remain underexplored. Here, we investigate the facultative anaerobe Paracoccus sanguinis, a Gram-negative bacterium isolated from human blood, and its metabolome, revealing insights into its potential impacts on health and disease. Using advanced analytical methods, we characterized 12 metabolites (1-12), including six novel compounds (1-3, 9, 10, and 12). Biosynthetic studies demonstrated that these metabolites are derived through enzymatic and nonenzymatic pathways. Functional evaluations revealed significant antiaging activities for 1, 6, and 11 in TNF-α-stimulated normal human dermal fibroblasts (NHDFs), including suppression of reactive oxygen species (ROS), inhibition of matrix metalloproteinase-1 (MMP-1) secretion, and reduction of inflammatory cytokines interleukin (IL)-6 and IL-8. Among the tested compounds, 11 exhibited the highest antiaging efficacy, highlighting its potential as a candidate for therapeutic applications targeting skin aging. This study elucidates the biosynthetic pathways of P. sanguinis metabolites and their antiskin aging activity, underscoring their potential in modulating skin health and offering novel insights into the functional roles of blood-derived microbiota in human health.},
}

@article {pmid40311618,
year = {2025},
author = {Andreu-Sánchez, S and Blanco-Míguez, A and Wang, D and Golzato, D and Manghi, P and Heidrich, V and Fackelmann, G and Zhernakova, DV and Kurilshikov, A and Valles-Colomer, M and Weersma, RK and Zhernakova, A and Fu, J and Segata, N},
title = {Global genetic structure of human gut microbiome species is related to geographic location and host health.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.04.014},
pmid = {40311618},
issn = {1097-4172},
abstract = {The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have associated microbial relative abundances with human-health-related phenotypes, the substantial intraspecies genetic variability of gut microbes has not yet been comprehensively considered, limiting the potential of linking such genetic traits with host conditions. Here, we analyzed 32,152 metagenomes from 94 microbiome studies across the globe to investigate the human microbiome intraspecies genetic diversity. We reconstructed 583 species-specific phylogenies and linked them to geographic information and species' horizontal transmissibility. We identified 484 microbial-strain-level associations with 241 host phenotypes, encompassing human anthropometric factors, biochemical measurements, diseases, and lifestyle. We observed a higher prevalence of a Ruminococcus gnavus clade in nonagenarians correlated with distinct plasma bile acid profiles and a melanoma and prostate-cancer-associated Collinsella clade. Our large-scale intraspecies genetic analysis highlights the relevance of strain diversity as it relates to human health.},
}

@article {pmid40304519,
year = {2025},
author = {Swayambhu, M and Gysi, M and Haas, C and Schuh, L and Walser, L and Javanmard, F and Flury, T and Ahannach, S and Lebeer, S and Hanssen, E and Snipen, L and Bokulich, NA and Kümmerli, R and Arora, N},
title = {Standardizing a microbiome pipeline for body fluid identification from complex crime scene stains.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0187124},
doi = {10.1128/aem.01871-24},
pmid = {40304519},
issn = {1098-5336},
abstract = {Recent advances in next-generation sequencing have opened up new possibilities for applying the human microbiome in various fields, including forensics. Researchers have capitalized on the site-specific microbial communities found in different parts of the body to identify body fluids from biological evidence. Despite promising results, microbiome-based methods have not been integrated into forensic practice due to the lack of standardized protocols and systematic testing of methods on forensically relevant samples. Our study addresses critical decisions in establishing these protocols, focusing on bioinformatics choices and the use of machine learning to present microbiome results in case reports for forensically relevant and challenging samples. In our study, we propose using operational taxonomic units (OTUs) for read data processing and generating heterogeneous training data sets for training a random forest classifier. We incorporated six forensically relevant classes: saliva, semen, skin from hand, penile skin, urine, and vaginal/menstrual fluid, and our classifier achieved a high weighted average F1 score of 0.89. Systematic testing on mock forensic samples, including mixed-source samples and underwear, revealed reliable detection of at least one component of the mixture and the identification of vaginal fluid from underwear substrates. Additionally, when investigating the sexually shared microbiome (sexome) of heterosexual couples, our classifier could potentially infer the nature of sexual activity. We therefore highlight the value of the sexome for assessing the nature of sexual activities in forensic investigations while delineating areas that warrant further research.IMPORTANCEMicrobiome-based analyses combined with machine learning offer potential avenues for use in forensic science and other applied fields, yet standardized protocols remain lacking. Moreover, machine learning classifiers have shown promise for predicting body sites in forensics, but they have not been systematically evaluated on complex mixed-source samples. Our study addresses key decisions for establishing standardized protocols and, to our knowledge, is the first to report classification results from uncontrolled mixed-source samples, including sexome (sexually shared microbiome) samples. In our study, we explore both the strengths and limitations of classifying the mixed-source samples while also providing options for tackling the limitations.},
}

@article {pmid40302548,
year = {2025},
author = {Singh, A and Mazumder, A and Das, S and Kanda, A and Tyagi, PK and Chaitanya, MVNL},
title = {Harnessing the Power of Probiotics: Boosting Immunity and Safeguarding against Various Diseases and Infections.},
journal = {Recent advances in anti-infective drug discovery},
volume = {20},
number = {1},
pages = {5-29},
pmid = {40302548},
issn = {2772-4352},
mesh = {*Probiotics/administration & dosage/therapeutic use ; Humans ; Animals ; Gastrointestinal Microbiome/immunology ; *Virus Diseases/immunology/prevention & control ; },
abstract = {The human microbiome, a diverse microorganism community, crucially defends against pathogens. Probiotics, postbiotics, and paraprobiotics alone and in combination are potent in countering fungal and waterborne infections, particularly against viral threats. This review focuses on the mechanisms of the microbiome against viral infections, emphasizing probiotic interventions. Certain Lactic Acid Bacteria (LAB) strains effectively eliminate toxic aflatoxin B1 (AFB1) from microfungi-produced mycotoxins. LAB binding to AFB1 persists post-gastric digestion, and pre-incubation with mycotoxins reduces probiotic adhesion to mucus. Oral probiotic administration in animals increases mycotoxin excretion, reducing associated health risks. Bifidobacterium longum and Lactobacillus rhamnosus show exceptional efficacy in removing cyanobacterial toxin microcystin-LR from drinking water. Engineered probiotics promise advanced therapeutic applications for metabolic disorders, Alzheimer's, and type 1 diabetes, serving as diagnostic tools for detecting pathogens and inflammation markers. In antimicrobial peptide production, genetically modified probiotics producing human β-defensin 2 (HBD2) treat Crohn's disease with implemented biocontainment strategies preventing unintended environmental impacts.},
}

*Probiotics/administration & dosage/therapeutic use
Humans
Animals
Gastrointestinal Microbiome/immunology
*Virus Diseases/immunology/prevention & control

@article {pmid40301726,
year = {2025},
author = {Yao, C and Zhang, Y and You, L and E, J and Wang, J},
title = {Comparative analysis of three experimental methods for revealing human fecal microbial diversity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {258},
pmid = {40301726},
issn = {1471-2180},
support = {2024L154//the Fundamental Research Program of Shanxi Province/ ; 202403021212101//the Science and Technology Innovation Project of Shanxi Provincial Universities/ ; 2018ZD14//the Major Program of Natural Science Foundation of Inner Mongolia/ ; },
abstract = {Due to the heterogeneity of the human gut environment, the gut microbiota is complex and diverse, and has been insufficiently explored. In this study, one fresh fecal sample was cultured using 12 commercial or modified media and incubation of culture plates anaerobically and aerobically, the conventional experienced colony picking (ECP) was first used to isolate the colonies and obtain pure culture strains. On this basis, all the colonies grown on the culture plates were collected for culture-enriched metagenomic sequencing (CEMS), and the original sample was also subjected to direct culture-independent metagenomic sequencing (CIMS), the study compared the effects of three methods for analyzing the microbiota contained in the sample. It was found that compared with CEMS, conventional ECP failed to detect a large proportion of strains grown in culture media, resulting in missed detection of culturable microorganisms in the gut. Microbes identified by CEMS and CIMS showed a low degree of overlap (18% of species), whereas species identified by CEMS and CIMS alone accounted for 36.5% and 45.5%, respectively. It suggests that both culture-dependent and culture-independent approaches are essential in revealing gut microbial diversity. Moreover, based on the CEMS results, growth rate index (GRiD) values for various strains on different media were calculated to predict the optimal medium for bacterial growth; this method can be used to design new media for intestinal microbial isolation, promote the recovery of specific microbiota, and obtain new insights into the human microbiome diversity. This is among the first studies on CEMS of the human gut microbiota.},
}

@article {pmid40299456,
year = {2025},
author = {Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Kozhakhmetova, S and Morenko, M and Duisebayeva, A and Poddighe, D and Kushugulova, A and Kozhakhmetov, S},
title = {Alterations in Gut Microbiota of Infants Born to Mothers with Obesity.},
journal = {Biomedicines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/biomedicines13040838},
pmid = {40299456},
issn = {2227-9059},
support = {Grant No. AP19575153 "Metagenomic predictors of childhood obesity, cross-talk with maternal mi-croflora", Grant No. AP23489538 and Grant No. BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Grant No. 20122022CRP1602//Nazarbayev University under Collaborative Research Program/ ; },
abstract = {Background: The impact of maternal obesity on offspring health remains a major and pressing issue. We investigated its impact on the development of the infant gut microbiome during the first six months of life, examining the taxonomic composition, metabolic pathways, and antibiotic resistance genes. Methods: Twenty-four mother-infant pairs were divided into maternally obese (OB, BMI > 36) and normal weight (BM) groups. Shotgun metagenomic sequencing was performed on stool samples collected at birth and at 1, 3, and 6 months. A total of 12 maternal samples and 23 infant samples (n = 35) in the obese group and 12 maternal samples and 30 infant samples (n = 42) in the control group were sequenced. The analysis included taxonomic profiling (MetaPhlAn 4), metabolic pathway analysis (HUMAnN 3), and antibiotic resistance gene screening (CARD/ABRicate). Results: The OB group showed reduced alpha diversity in the first month (p ≤ 0.01) and an increased Firmicutes/Bacteroidetes ratio, peaking at 3 months (p ≤ 0.001). The metabolic profiling revealed enhanced carbohydrate breakdown (p ≤ 0.001) in the BM group and lipid biosynthesis (p ≤ 0.0001) in the OB group pathways. Strong correlations emerged between Lactobacillales and fatty acid biosynthesis (r = 0.7, p ≤ 0.0001) and between Firmicutes and lincosamide (r = 0.8, p ≤ 0.0001). Conclusions: The infants of obese mothers had significantly altered development of the infant gut microbiome, affecting both composition and metabolic potential. These changes may have long-term health consequences and suggest potential therapeutic targets for intervention.},
}

@article {pmid40298367,
year = {2025},
author = {Zhou, Z and Ma, Y and Zhang, D and Ji, R and Wang, Y and Zhao, J and Ma, C and Zhu, H and Shen, H and Jiang, X and Niu, Y and Lu, J and Zhang, B and Tu, L and Zhang, H and Ma, X and Chen, P},
title = {Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0027625},
doi = {10.1128/msystems.00276-25},
pmid = {40298367},
issn = {2379-5077},
abstract = {Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.},
}

@article {pmid40297591,
year = {2025},
author = {Pei, X and Liu, L and Han, Y},
title = {Advances in human microbiome and prostate cancer research.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1576679},
pmid = {40297591},
issn = {1664-3224},
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology ; Male ; *Microbiota ; *Gastrointestinal Microbiome ; Tumor Microenvironment/immunology ; Animals ; },
abstract = {Prostate cancer (PCa) is the second most common malignant tumor in men worldwide, and its metastatic and heterogeneous nature makes it significantly more difficult to treat. Recent studies have revealed the critical role of microbiota in PCa occurrence, progression, and treatment. Accumulating evidence from 16S rRNA and metagenomic sequencing suggests the presence of specific microbiota in prostate tissues and macrogenomics techniques: cancerous tissues are enriched with pro-inflammatory genera (e.g., Fusobacterium, Propionibacterium acnes), whereas commensal bacteria (e.g., Pseudomonas) are more common in paracancerous tissues. The microbiota drive tumor progression through activation of the NF-κB/STAT3 pathway to induce chronic inflammation, modulation of the immune microenvironment (e.g., Treg/Th17 imbalance and M2-type macrophage polarization), and metabolite (e.g., LPS, short-chain fatty acids)-mediated hormonal and epigenetic regulation. In terms of clinical translation, urinary microbiota characterization combined with metabolomics analysis may enhance diagnostic specificity, while gut flora modulation (e.g., probiotic interventions or fecal transplants) may improve resistance to androgen deprivation therapy. Current challenges include sequencing accuracy of low-biomass samples, limitations of causal mechanism validation models, and large cohort heterogeneity. In the future, it will be necessary to integrate multi-omics technologies to explore the bidirectional regulation of the "gut-prostate axis" and develop personalized therapeutic strategies targeting microorganisms. In this paper, we systematically review the interactions between microbiota and PCa and their clinical potentials to provide a theoretical basis for precision diagnosis and treatment.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/immunology/metabolism/etiology
Male
*Microbiota
*Gastrointestinal Microbiome
Tumor Microenvironment/immunology
Animals

@article {pmid40296251,
year = {2025},
author = {Zheng, H and Chen, Y and Lu, S and Liu, Z and Ma, Y and Zhang, C and Zhang, Y and Zhang, J and Liu, C and Chu, M and Pei, F and Liu, S and Duan, L},
title = {Mechanosensory Piezo2 regulated by gut microbiota participates in the development of visceral hypersensitivity and intestinal dysmotility.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2497399},
doi = {10.1080/19490976.2025.2497399},
pmid = {40296251},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; Humans ; Mice ; *Irritable Bowel Syndrome/microbiology/physiopathology/metabolism/therapy ; *Ion Channels/metabolism/genetics ; Male ; Female ; Fecal Microbiota Transplantation ; *Gastrointestinal Motility ; Adult ; Middle Aged ; Colon/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Fusobacterium/physiology ; Dysbiosis/microbiology ; Disease Models, Animal ; Ganglia, Spinal/metabolism ; Akkermansia ; },
abstract = {The gut microbiota plays a crucial role in the manifestation of intestinal dysfunction associated with irritable bowel syndrome (IBS). The mechanosensory Piezo2 has been implicated in the regulation of intestinal function. However, it remains unclear whether Piezo2 is modulated by the gut microbiota, thus contributing to the development of visceral hypersensitivity and gut dysmotility. The study enrolled patients with diarrhea-predominant IBS (IBS-D) alongside healthy controls (HC). Questionnaires, rectal barostat test, and colonoscopy with mucosal biopsy were conducted. Fecal microbiota transplantation (FMT) was performed using samples from HC or IBS-D patients, and interventions with Akkermansia muciniphila or Fusobacterium varium were carried out on colon- or dorsal root ganglion (DRG)- Piezo2 knockdown pseudo-germ-free mice. Visceral sensitivity and intestinal motility were assessed. Piezo2 levels were detected using western blot and immunofluorescence. Fecal 16S rRNA sequencing and cecum untargeted metabolomics analysis, followed by molecular docking predictions of Piezo2, were also performed. The ratio of Piezo2[+]/5-HT[+] cells was lower in IBS-D patients, positively correlated with visceral sensation and intestinal dysbiosis. The mice that received FMT from IBS-D patients exhibited colonic dysmotility and visceral hypersensitivity, along with elevated Piezo2 protein levels in the colon and DRG. Knockdown of Piezo2 in the colon or DRG ameliorated the FMT-induced colonic dysmotility and visceral hypersensitivity. Fecal 16S rRNA sequencing revealed distinct microbiota composition. Notably, Fusobacterium varium, but not Akkermansia muciniphila, induced gut dysmotility and visceral hypersensitivity, effects that could be alleviated by colon or DRG Piezo2 knockdown. Additionally, Fusobacterium varium lead to increased Piezo2 protein levels, as well as elevated levels of indole-3-acetic acid and indole-3-acrylic acid, which were predicted to bind to Piezo2, causing disturbances. Piezo2 can be regulated by gut microbiota and involved in visceral hypersensitivity and colonic dysmotility, with Fusobacterium varium playing a crucial role.},
}

*Gastrointestinal Microbiome/physiology
Animals
Humans
Mice
*Irritable Bowel Syndrome/microbiology/physiopathology/metabolism/therapy
*Ion Channels/metabolism/genetics
Male
Female
Fecal Microbiota Transplantation
*Gastrointestinal Motility
Adult
Middle Aged
Colon/metabolism
Mice, Inbred C57BL
Feces/microbiology
Fusobacterium/physiology
Dysbiosis/microbiology
Disease Models, Animal
Ganglia, Spinal/metabolism
Akkermansia

@article {pmid40296128,
year = {2025},
author = {Adlakha, YK and Chhabra, R},
title = {The human microbiome: redefining cancer pathogenesis and therapy.},
journal = {Cancer cell international},
volume = {25},
number = {1},
pages = {165},
pmid = {40296128},
issn = {1475-2867},
abstract = {The human microbiome has always been an important determinant of health and recently, its role has also been described in cancer. The altered microbiome could aid cancer progression, modulate chemoresistance and significantly alter drug efficacy. The broad implications of microbes in cancer have prompted researchers to investigate the microbe-cancer axis and identify whether modifying the microbiome could sensitize cancer cells for therapy and improve the survival outcome of cancer patients. The preclinical data has shown that enhancing the number of specific microbial species could restore the patients' response to cancer drugs and the microbial biomarkers may play a vital role in cancer diagnostics. The elucidation of detailed interactions of the human microbiota with cancer would not only help identify the novel drug targets but would also enhance the efficacy of existing drugs. The field exploring the emerging roles of microbiome in cancer is at a nascent stage and an in-depth scientific perspective on this topic would make it more accessible to a wider audience. In this review, we discuss the scientific evidence connecting the human microbiome to the origin and progression of cancer. We also discuss the potential mechanisms by which microbiota affects initiation of cancer, metastasis and chemoresistance. We highlight the significance of the microbiome in therapeutic outcome and evaluate the potential of microbe-based cancer therapy.},
}

@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 {pmid40264322,
year = {2025},
author = {Jain, MS and Prasanthi, S and Bommala, ND and Goudanavar, P and Naveen, NR},
title = {Harnessing the Human Microbiome for Innovative Drug Delivery Systems: Exploring Pharmacomicrobiomics and Targeted Therapies.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128354250250326045943},
pmid = {40264322},
issn = {1873-4286},
abstract = {The human gut microbiome has emerged as a crucial component of health and disease, presenting novel opportunities for the development of drug delivery systems based on microbiome interactions. This paper explores advanced strategies utilizing microorganisms, engineered bacteria, viruses, and bacteria-encapsulated nanoparticles as next-generation therapeutic vehicles. Focusing on analytical approaches to phage therapy and bio-hybrid bacteria for targeted drug delivery, the article highlights recent breakthroughs in colon-specific targeting for gastrointestinal disorders. The study also delves into the emerging field of pharmacomicrobiomics, with an emphasis on applications in cancer, cardiovascular, digestive, and nervous system treatments, specifically targeting key drug classes such as ACE inhibitors, proton-pump inhibitors, and NSAIDs. Challenges related to cytotoxicity and toxicity are addressed, offering proposals for safer therapeutic applications. This review underscores the transformative potential of the microbiome in personalized medicine and targeted drug delivery, with a focus on its integration with advanced technologies to optimize therapeutic outcomes.},
}

@article {pmid40261032,
year = {2025},
author = {Cho, M-Y and Eom, J-H and Choi, E-M and Yang, S-J and Lee, D and Kim, YY and Kim, H-S and Hwang, I},
title = {Recent advances in therapeutic probiotics: insights from human trials.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0024024},
doi = {10.1128/cmr.00240-24},
pmid = {40261032},
issn = {1098-6618},
abstract = {SUMMARYRecent advances in therapeutic probiotics have shown promising results across various health conditions, reflecting a growing understanding of the human microbiome's role in health and disease. However, comprehensive reviews integrating the diverse therapeutic effects of probiotics in human subjects have been limited. By analyzing randomized controlled trials (RCTs) and meta-analyses, this review provides a comprehensive overview of key developments in probiotic interventions targeting gut, liver, skin, vaginal, mental, and oral health. Emerging evidence supports the efficacy of specific probiotic strains and combinations in treating a wide range of disorders, from gastrointestinal (GI) and liver diseases to dermatological conditions, bacterial vaginosis, mental disorders, and oral diseases. We discuss the expanding understanding of microbiome-organ connections underlying probiotic mechanisms of action. While many clinical trials demonstrate significant benefits, we acknowledge areas requiring further large-scale studies to establish definitive efficacy and optimal treatment protocols. The review addresses challenges in standardizing probiotic research methodologies and emphasizes the importance of considering individual variations in microbiome composition and host genetics. Additionally, we explore emerging concepts such as the oral-gut-brain axis and future directions, including high-resolution microbiome profiling, host-microbe interaction studies, organoid models, and artificial intelligence applications in probiotic research. Overall, this review offers a comprehensive update on the current state of therapeutic probiotics across multiple domains of human health, providing insights into future directions and the potential for probiotics to revolutionize preventive and therapeutic medicine.},
}

@article {pmid40257583,
year = {2025},
author = {Hu, J and Chen, W and Zhu, R and Yang, F and Xu, J and Xiang, B and Li, Y and Wang, W and Zhu, L and Chen, G and Zhi, M},
title = {Correction: Dietary risk factors in Crohn's disease and ulcerative colitis: a cohort study with paired healthy relatives as controls.},
journal = {European journal of nutrition},
volume = {64},
number = {4},
pages = {161},
doi = {10.1007/s00394-025-03669-y},
pmid = {40257583},
issn = {1436-6215},
}

@article {pmid40253432,
year = {2025},
author = {Kelliher, JM and Aljumaah, M and Bordenstein, SR and Brister, JR and Chain, PSG and Dundore-Arias, JP and Emerson, JB and Fernandes, VMC and Flores, R and Gonzalez, A and Hansen, ZA and Hatcher, EL and Jackson, SA and Kellogg, CA and Madupu, R and Miller, CML and Mirzayi, C and Moustafa, AM and Mungall, C and Oliver, A and Pariente, N and Pett-Ridge, J and Record, S and Reji, L and Reysenbach, AL and Rich, VI and Richardson, L and Schriml, LM and Shabman, RS and Sierra, MA and Sullivan, MB and Sundaramurthy, P and Thibault, KM and Thompson, LR and Tighe, S and Vereen, E and Eloe-Fadrosh, EA},
title = {Microbiome data management in action workshop: Atlanta, GA, USA, June 12-13, 2024.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {40},
pmid = {40253432},
issn = {2524-6372},
support = {2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; 2422717//Directorate for Biological Sciences/ ; },
abstract = {Microbiome research is revolutionizing human and environmental health, but the value and reuse of microbiome data are significantly hampered by the limited development and adoption of data standards. While several ongoing efforts are aimed at improving microbiome data management, significant gaps still remain in terms of defining and promoting adoption of consensus standards for these datasets. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines for human microbiome research have been endorsed and successfully utilized by many research organizations, publishers, and funding agencies, and have been recognized as a consensus community standard. No equivalent effort has occurred for environmental, synthetic, and non-human host-associated microbiomes. To address this growing need within the microbiome research community, we convened the Microbiome Data Management in Action Workshop (June 12-13, 2024, in Atlanta, GA, USA), to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. The 50 attendees, representing the diverse and interdisciplinary nature of microbiome research, discussed recent progress and challenges, and brainstormed actionable recommendations and paths forward for coordinated environmental microbiome data management and the modifications necessary for the STORMS guidelines to be applied to environmental, non-human host, and synthetic microbiomes. The outcomes of this workshop will form the basis of a formalized data management roadmap to be implemented across the field. These best practices will drive scientific innovation now and in years to come as these data continue to be used not only in targeted reanalyses but in large-scale models and machine learning efforts.},
}

@article {pmid40251928,
year = {2025},
author = {Boem, F and Lamminpää, I and Amedei, A},
title = {Updating the Discontinuity Theory to the Extended Immunity: The Symmunobiome Concept.},
journal = {European journal of immunology},
volume = {55},
number = {4},
pages = {e202451528},
doi = {10.1002/eji.202451528},
pmid = {40251928},
issn = {1521-4141},
support = {PE0000006//Italian Ministry of University and Research MNESYS/ ; B55F2100//University of Florence-European Union-Next Generation EU-CUP/ ; B83C22003920001//The National Recovery and Resilience Plan, Investment 1.5 Ecosystems of Innovation, Project Tuscany Health Ecosystem (THE), CUP/ ; },
mesh = {Humans ; *Microbiota/immunology ; Animals ; *Immune System/immunology ; Symbiosis/immunology ; Homeostasis/immunology ; *Immunity ; Biological Evolution ; Immunity, Innate ; Adaptive Immunity ; },
abstract = {The immune system (IS) is commonly understood as a system composed of specific cells and tissues that have evolved to contrast pathogens and defend the host. By virtue of this capacity, it has come to be considered capable of making an essential distinction, that between self versus non-self, which would contribute to a clear identity of the organism. However, in the wake of evolution and ecology, growing evidence suggests that the so-called immune system, which also evolved from symbiotic interactions with external agents, is not just a defensive system that merely protects the organism but, on the contrary, is involved in many global regulatory and homeostatic functions. Moreover, in performing these many functions, IS is not only an ensemble of host cells and tissues but functionally is constitutively determined by the interaction with a set of associated microorganisms, that is, the human microbiome. In this scenario, it is open-and-shut that the microbiome itself is a functional part of this extended immune system. Organisms and microbiomes together, therefore, form a functional whole, which constitutes a privileged form of biological organization. In light of this evidence showing the inadequacy of traditional accounts, we propose to extend and supplement the current IS conceptualization by introducing the notion of the symmunobiome. With this term, we intend to characterize the microbiome's own and unavoidable component to overall immune functionality. Therefore, we suggest a new immune system determination, articulated in three linked pillars-adaptive immunity, innate immunity, and symmunobiome-to better grasp the diverse functionality of extended immunity.},
}

Humans
*Microbiota/immunology
Animals
*Immune System/immunology
Symbiosis/immunology
Homeostasis/immunology
*Immunity
Biological Evolution
Immunity, Innate
Adaptive Immunity

@article {pmid40246834,
year = {2025},
author = {Beaudoin, CA and Norget, S and Omran, Z and Hala, S and Daqeeq, AH and Burnet, PWJ and Blundell, TL and van Tonder, AJ},
title = {Similarity of drug targets to human microbiome metaproteome promotes pharmacological promiscuity.},
journal = {The pharmacogenomics journal},
volume = {25},
number = {3},
pages = {9},
pmid = {40246834},
issn = {1473-1150},
support = {ANTSRG 01/2019//Antibiotic Research UK (ANTRUK)/ ; },
mesh = {Humans ; Female ; *Microbiota/drug effects/genetics ; *Proteome/genetics ; *Gastrointestinal Microbiome/drug effects ; Vagina/microbiology ; Proteomics/methods ; Mouth/microbiology ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {Similarity between candidate drug targets and human proteins is commonly assessed to minimize the occurrence of side effects. Although numerous drugs have been found to disrupt the health of the human microbiome, no comprehensive comparison between established drug targets and the human microbiome metaproteome has yet been conducted. Therefore, herein, sequence and structure alignments between human and pathogen drug targets and representative human gut, oral, and vaginal microbiome metaproteomes were performed. Both human and pathogen drug targets were found to be similar in sequence, function, structure, and drug binding capacity to proteins in diverse pathogenic and non-pathogenic bacteria from all three microbiomes. The gut metaproteome was identified as particularly susceptible overall to off-target effects. Certain symptoms, such as infections and immune disorders, may be more common among drugs that non-selectively target host microbiota. These findings suggest that similarities between human microbiome metaproteomes and drug target candidates should be routinely checked.},
}

Humans
Female
*Microbiota/drug effects/genetics
*Proteome/genetics
*Gastrointestinal Microbiome/drug effects
Vagina/microbiology
Proteomics/methods
Mouth/microbiology
Bacteria/drug effects/genetics/metabolism

@article {pmid40243330,
year = {2025},
author = {Walker, AR and Pham, DN and Noeparvar, P and Peterson, AM and Lipp, MK and Lemos, JA and Zeng, L},
title = {Fructose activates a stress response shared by methylglyoxal and hydrogen peroxide in Streptococcus mutans.},
journal = {mBio},
volume = {},
number = {},
pages = {e0048525},
doi = {10.1128/mbio.00485-25},
pmid = {40243330},
issn = {2150-7511},
abstract = {Fructose catabolism by Streptococcus mutans is initiated by three phosphotransferase (PTS) transporters yielding fructose-1-phosphate (F-1-P) or fructose-6-phosphate. Deletion of one such F-1-P-generating PTS, fruI, was shown to reduce the cariogenicity of S. mutans in rats fed a high-sucrose diet. Moreover, a recent study linked fructose metabolism in S. mutans to a reactive electrophile species methylglyoxal. Here, we conducted a comparative transcriptomic analysis of S. mutans treated briefly with 50 mM fructose, 50 mM glucose, 5 mM methylglyoxal, or 0.5 mM hydrogen peroxide (H2O2). The results revealed a striking overlap between the fructose and methylglyoxal transcriptomes, totaling 176 genes, 61 of which were also shared with the H2O2 transcriptome. This core of 61 genes encompassed many of the same pathways affected by exposure to low pH or zinc intoxication. Consistent with these findings, fructose negatively impacted the metal homeostasis of a mutant deficient in zinc expulsion and the growth of a mutant of the major oxidative stress regulator SpxA1. Importantly, fructose metabolism lowered culture pH at a faster pace, allowed better survival under acidic and nutrient-depleted conditions, and enhanced the competitiveness of S. mutans against Streptococcus sanguinis, although a moderated level of F-1-P might further boost some of these benefits. Conversely, several commensal streptococcal species displayed a greater sensitivity to fructose that may negatively affect their persistence and competitiveness in dental biofilm. In conclusion, fructose metabolism is integrated into the stress core of S. mutans and regulates critical functions required for survival and its ability to induce dysbiosis in the oral cavity.IMPORTANCEFructose is a common monosaccharide in the biosphere, yet its overconsumption has been linked to various health problems in humans including insulin resistance, obesity, diabetes, non-alcoholic liver diseases, and even cancer. These effects are in large part attributable to the unique biochemical characteristics and metabolic responses associated with the degradation of fructose. Yet, an understanding of the effects of fructose on the physiology of bacteria and its implications for the human microbiome is severely lacking. Here, we performed a series of analyses on the gene regulation of a dental pathogen Streptococcus mutans by exposing it to fructose and other important stress agents. Further supported by growth, persistence, and competition assays, our findings revealed the ability of fructose to activate a set of stress-related functions that may prove critical to the ability of the bacterium to persist and cause diseases both within and without the oral cavity.},
}

@article {pmid40238826,
year = {2025},
author = {Lee, J and Kim, B},
title = {Zero inflated high dimensional compositional data with DeepInsight.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320832},
doi = {10.1371/journal.pone.0320832},
pmid = {40238826},
issn = {1932-6203},
mesh = {Humans ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Neural Networks, Computer ; Inflammatory Bowel Diseases/microbiology ; Child ; },
abstract = {Through the Human Microbiome Project, research on human-associated microbiomes has been conducted in various fields. New sequencing techniques such as Next Generation Sequencing (NGS) and High-Throughput Sequencing (HTS) have enabled the inclusion of a wide range of features of the microbiome. These advancements have also contributed to the development of numerical proxies like Operational Taxonomic Units (OTUs) and Amplicon Sequence Variants (ASVs). Studies involving such microbiome data often encounter zero-inflated and high-dimensional problems. Based on the need to address these two issues and the recent emphasis on compositional interpretation of microbiome data, we conducted our research. To solve the zero-inflated problem in compositional microbiome data, we transformed the data onto the surface of the hypersphere using a square root transformation. Then, to solve the high-dimensional problem, we modified DeepInsight, an image-generating method using Convolutional Neural Networks (CNNs), to fit the hypersphere space. Furthermore, to resolve the common issue of distinguishing between true zero values and fake zero values in zero-inflated images, we added a small value to the true zero values. We validated our approach using pediatric inflammatory bowel disease (IBD) fecal sample data and achieved an area under the curve (AUC) value of 0.847, which is higher than the previous study's result of 0.83.},
}

Humans
High-Throughput Nucleotide Sequencing/methods
*Microbiota/genetics
Neural Networks, Computer
Inflammatory Bowel Diseases/microbiology
Child

@article {pmid40237489,
year = {2025},
author = {Rybicka, I and Kaźmierczak, Z},
title = {The human phageome: niche-specific distribution of bacteriophages and their clinical implications.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178824},
doi = {10.1128/aem.01788-24},
pmid = {40237489},
issn = {1098-5336},
abstract = {Bacteriophages (phages) play a crucial role in shaping the composition and diversity of the human microbiome across various body niches. Recent advancements in high-throughput sequencing technologies have enabled comprehensive analysis of the human phageome in different body sites. This review comprehensively analyzes phage populations across major human body niches, examining their distribution and dynamics through recent metagenomic discoveries. We explore how phage-bacteria interactions within different body sites contribute to homeostasis and disease development. Emerging evidence demonstrates that phageome perturbations can serve as early indicators of various disorders, particularly in the gut microbiome. Understanding these complex microbial interactions offers promising opportunities for developing novel diagnostic markers and therapeutic approaches. However, the causal relationship between phages, bacteria, and disease development remains unclear. Further research is needed to elucidate the role of phages in human health and disease and to explore their potential as diagnostic or therapeutic tools. Understanding the intricate interactions between phages, bacteria, and the human host is crucial for unraveling the complexities of the human microbiome and its impact on health and disease.},
}

@article {pmid40237447,
year = {2025},
author = {Choudoir, MJ and Ishaq, SL and Beiko, RG and Silva, DS and Allen-Vercoe, E and O'Doherty, KC},
title = {The case for microbiome stewardship: what it is and how to get there.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006225},
doi = {10.1128/msystems.00062-25},
pmid = {40237447},
issn = {2379-5077},
abstract = {Microbiomes are essential for human, animal, plant, and ecosystem health. Despite widespread recognition of the importance of microbiomes, there is little attention paid to monitoring and safeguarding microbial ecologies on policy levels. We observe that microbiomes are deteriorating owing to practices at societal levels such as pesticide use in agriculture, air and water pollution, and overuse of antibiotics. Potential policy on these issues would cross multiple domains such as public health, environmental protection, and agriculture. We propose microbiome stewardship as a foundational concept that can act across policy domains to facilitate healthy microbiomes for human and ecosystem health. We examine challenges to be addressed and steps to take toward developing meaningful microbiome stewardship.},
}

@article {pmid40236770,
year = {2025},
author = {Zhang, C and Chen, Y and Duan, R and Zhang, Y and Zheng, H and Zhang, J and Zhang, T and Xu, J and Li, K and Pei, F and Duan, L},
title = {Preconception maternal gut dysbiosis affects enteric nervous system development and disease susceptibility in offspring via the GPR41-GDNF/RET/SOX10 signaling pathway.},
journal = {iMeta},
volume = {4},
number = {2},
pages = {e70012},
pmid = {40236770},
issn = {2770-596X},
abstract = {Maternal health, specifically changes in the gut microbiota, can profoundly impact offspring health; however, our understanding of how gut microbiota alterations during the preconception period influence the offspring remains limited. In this study, we investigated the impact and mechanisms of preconception maternal gut dysbiosis on the development of the enteric nervous system (ENS) in mice. We found that preconception maternal exposure to antibiotics led to the abnormal development of the ENS in offspring, increasing their susceptibility to water avoidance stress at the adult stage. Metagenomic, targeted metabolomic, and transcriptomic analyses revealed that preconception antibiotic exposure disrupted the expression of genes crucial for embryonic ENS development by altering maternal gut microbiota composition. Multi-omics analysis combined with Limosilactobacillus reuteri and propionate gestational supplementation demonstrated that the maternal gut microbiota and metabolites may influence embryonic ENS development via the GPR41-GDNF/RET/SOX10 signaling pathway. Our findings highlight the critical importance of maintaining a healthy maternal gut microbiota before conception to support normal ENS development in offspring.},
}

@article {pmid40235960,
year = {2025},
author = {Basgaran, A and Lymberopoulos, E and Burchill, E and Reis-Dehabadi, M and Sharma, N},
title = {Machine learning determines the incidence of Alzheimer's disease based on population gut microbiome profile.},
journal = {Brain communications},
volume = {7},
number = {2},
pages = {fcaf059},
pmid = {40235960},
issn = {2632-1297},
abstract = {The human microbiome is a complex and dynamic community of microbes, thought to have symbiotic benefit to its host. Influences of the gut microbiome on brain microglia have been identified as a potential mechanism contributing to neurodegenerative diseases, such as Alzheimer's disease, motor neurone disease and Parkinson's disease (Boddy SL, Giovannelli I, Sassani M, et al. The gut microbiome: A key player in the complexity of amyotrophic lateral sclerosis (ALS). BMC Med. 2021;19(1):13). We hypothesize that population level differences in the gut microbiome will predict the incidence of Alzheimer's disease using machine learning methods. Cross-sectional analyses were performed in R, using two large, open-access microbiome datasets (n = 959 and n = 2012). Countries in these datasets were grouped based on Alzheimer's disease incidence and the gut microbiome profiles compared. In countries with a high incidence of Alzheimer's disease, there is a significantly lower diversity of the gut microbiome (P < 0.05). A permutational analysis of variance test (P < 0.05) revealed significant differences in the microbiome profile between countries with high versus low incidence of Alzheimer's disease with several contributing taxa identified: at a species level Escherichia coli, and at a genus level Haemophilus and Akkermansia were found to be reproducibly protective in both datasets. Additionally, using machine learning, we were able to predict the incidence of Alzheimer's disease within a country based on the microbiome profile (mean area under the curve 0.889 and 0.927). We conclude that differences in the microbiome can predict the varying incidence of Alzheimer's disease between countries. Our results support a key role of the gut microbiome in neurodegeneration at a population level.},
}

@article {pmid40235735,
year = {2025},
author = {Xu, R and Yu, Y and Chen, T},
title = {Exploring the dark side of probiotics to pursue light: Intrinsic and extrinsic risks to be opportunistic pathogens.},
journal = {Current research in food science},
volume = {10},
number = {},
pages = {101044},
pmid = {40235735},
issn = {2665-9271},
abstract = {Probiotics, live microorganisms with multiple health benefits, have gained popularity for their roles in maintaining daily health and treating a variety of diseases. However, they have the potential to be opportunistic pathogens in some conditions. This review delves into the intrinsic and extrinsic risks associated with probiotics. Intrinsic risks involve the production of harmful substances, such as toxins and invasive factors, biofilm formation, bacteria emboli, antibiotic resistance with relevant genetic materials, genetic plasticity, and metabolic issues, while extrinsic risks include problems in regulatory oversight and public awareness, host health status and appropriately administration. It emphasizes the need for a balanced view of their therapeutic benefits and potential hazards, advocating for further research to understand the complex interactions between probiotics and the human microbiome, to optimize the safety and efficacy of probiotics.},
}

@article {pmid40231347,
year = {2025},
author = {Hoffmanns, L and Svedberg, D and Mateus, A},
title = {Protein O-glycosylation in the Bacteroidota phylum.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70041},
pmid = {40231347},
issn = {2211-5463},
support = {Wallenberg Academy Fellows 2025//Knut och Alice Wallenbergs Stiftelse/ ; 2021-06602//Vetenskapsrådet/ ; 2022-02958//Vetenskapsrådet/ ; ProFITGut-101076015//H2020 European Research Council/ ; },
abstract = {Glycans play crucial roles in bacteria, such as providing structural integrity or enabling interactions with the ecosystem. They can be linked to lipids, peptides, or proteins. In proteins, they modify either asparagine (N-glycosylation) or serine or threonine (O-glycosylation). Species of the Bacteroidota phylum, a major component of the human microbiome and marine and soil ecosystems, have a unique type of O-glycosylation that modifies multiple noncytoplasmic proteins containing a specific amino acid sequence. Only a small number of species have currently been characterized, but within one species, generally all proteins are modified with the same glycan structure. Most species share a common inner part but differ in the sugar composition and branching of the outer part of their glycan. This suggests that the biosynthesis of the glycan occurs in two separate steps. Both the inner core and the outer glycan are likely assembled from nucleotide-activated monosaccharides on undecaprenyl phosphate on the cytoplasmic side of the inner membrane, prior to being flipped to the periplasm and transferred to the protein. A genomic locus responsible for the biosynthesis of the outer glycan has been identified, containing some conserved genes across species. Despite substantial progress in the characterization of this O-glycosylation system, its function, the overall diversity of glycan structures across the phylum, and the complete biosynthetic pathway remain mostly unknown. Due to the importance of this group of species for the human gut microbiome, elucidating these aspects can open up strategies to modulate the composition of the microbiome community toward a healthy state.},
}

@article {pmid40229539,
year = {2025},
author = {Magne, F and Ruiz-Ruiz, S and Pérez-Brocal, V and Ponce, CA and Bustamante, R and Martin, VS and Gutierrez, M and Gatti, G and Vargas, SL and Moya, A},
title = {Pneumocystis jirovecii is a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {609},
pmid = {40229539},
issn = {2399-3642},
mesh = {Humans ; Infant ; *Microbiota ; *Lung/microbiology ; Female ; *Pneumocystis carinii/physiology/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Infant, Newborn ; },
abstract = {Early life gut microbiota is being increasingly recognized as a major contributor to short and/or long-term human health and diseases. However, little is known about these early-life events in the human microbiome of the lower respiratory tract. This study aims to investigate fungal and bacterial colonization in the lower airways over the first year of life by analyzing lung tissue from autopsied infants. The fungal and bacterial communities of lung tissue samples from 53 autopsied infants were characterized by Next-Generation Sequencing (NGS), based on universal PCR amplification of the ITS region and the 16S rRNA gene, respectively. Our study highlights a high degree of inter-individual variability in both fungal and bacterial communities inhabiting the infant lung. The lower respiratory tract microbiota is mainly composed of transient microorganisms that likely travel from the upper respiratory tract and do not establish permanent residence. However, it could also contain some genera identified as long-term inhabitants of the lung, which could potentially play a role in lung physiology or disease. At 3-4 months of age, important dynamic changes to the microbial community were observed, which might correspond to a transitional time period in the maturation of the lung microbiome. This timeframe represents a susceptibility period for the colonization of pathogens such as Pneumocystis. The asymptomatic colonization of Pneumocystis was associated with changes in the fungal and bacterial communities. These findings suggest that the period of 2-4 months of age is a "critical window" early in life. Pneumocystis jirovecii could be a potential pivotal ecological driver contributing to shifts in microbial equilibrium during the early-life lower airway microbiome assembly, and to the future health of children.},
}

Humans
Infant
*Microbiota
*Lung/microbiology
Female
*Pneumocystis carinii/physiology/genetics
Male
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Infant, Newborn

@article {pmid40227812,
year = {2025},
author = {Leigh, J and Skidmore, B and Wong, A and Maleki Vareki, S and Ng, TL},
title = {Exploring the Microbiome's Impact on Glioma and Brain Metastases: Insights into Development, Progression, and Treatment Response-A Scoping Review.},
journal = {Cancers},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/cancers17071228},
pmid = {40227812},
issn = {2072-6694},
abstract = {Background: The human microbiome plays a crucial role in health and disease. Dysbiosis, an imbalance of microorganisms, has been implicated in cancer development and treatment response, including in primary brain tumors and brain metastases, through interactions mediated by the gut-brain axis. This scoping review synthesizes current evidence on the relationship between the human microbiome and brain tumors. Methods: A systematic search of five electronic databases was conducted by an expert librarian, using controlled vocabulary and keywords. A targeted grey literature search in Google Scholar and clinical trial registries was also undertaken. Eligible studies included primary research involving human patients, or in vivo, or in vitro models of glioma or brain metastasis, with a focus on the microbiome's role in tumor development, treatment response, and outcomes. Results: Out of 584 citations screened, 40 studies met inclusion criteria, comprising 24 articles and 16 conference abstracts. These included 12 human studies, 16 using mouse models, 7 combining both, and 5 employing large datasets or next-generation sequencing of tumor samples. Thirty-one studies focused on primary brain tumors, six on brain metastases, and three on both. Of the 20 studies examining dysbiosis in tumor development, 95% (n = 19) found an association with tumor growth. Additionally, 71.4% (n = 5/7) of studies reported that microbiome alterations influenced treatment efficacy. Conclusions: Although the role of the gut-brain axis in brain tumors is still emerging and is characterized by heterogeneity across studies, existing evidence consistently supports a relationship between the gut microbiome and both brain tumor development and treatment outcomes.},
}

@article {pmid40219702,
year = {2025},
author = {Xiao, Y and Yue, X and Zhang, X and Yang, Y and Zhang, Y and Sun, L},
title = {The role of bacteriophage in inflammatory bowel disease and its therapeutic potential.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2025.2492154},
pmid = {40219702},
issn = {1549-7828},
abstract = {Inflammatory bowel disease (IBD) refers to a group of chronic inflammatory disorders impacting the gastrointestinal (GI) tract. It represents a significant public health challenge due to its rising global incidence and substantial impact on patients' quality of life. Emerging research suggests a pivotal role of the human microbiome in IBD pathogenesis. Bacteriophages, integral components of the human microbiome, are indicated to influence the disease onset, progression, and therapeutic strategies. Here, we review the effect of bacteriophages on the pathogenesis of IBD and, more specifically, on the gut bacteria, the systemic immunity, and the susceptibility genes. Additionally, we explore the potential therapeutic use of the bacteriophages to modify gut microbiota and improve the health outcomes of IBD patients. This review highlights the potential of therapeutic bacteriophages in regulating gut microbiota and modulating the immune response to improve health outcomes in IBD patients. Future studies on personalized bacteriophage therapy and its integration into clinical practice could advance treatment strategies for IBD.},
}

@article {pmid40214493,
year = {2025},
author = {Rahim, MA and Seo, H and Barman, I and Hossain, MS and Shuvo, MSH and Song, HY},
title = {Insights into Autophagy in Microbiome Therapeutic Approaches for Drug-Resistant Tuberculosis.},
journal = {Cells},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/cells14070540},
pmid = {40214493},
issn = {2073-4409},
support = {RS-2023-00219563//National Research Foundation of Korea/ ; P248400003//Korea Institute for Advancement of Technology (KIAT)/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
mesh = {Humans ; *Autophagy ; *Tuberculosis, Multidrug-Resistant/therapy/microbiology ; *Microbiota ; Mycobacterium tuberculosis/drug effects ; Animals ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {Tuberculosis, primarily caused by Mycobacterium tuberculosis, is an airborne lung disease and continues to pose a significant global health threat, resulting in millions of deaths annually. The current treatment for tuberculosis involves a prolonged regimen of antibiotics, which leads to complications such as recurrence, drug resistance, reinfection, and a range of side effects. This scenario underscores the urgent need for novel therapeutic strategies to combat this lethal pathogen. Over the last two decades, microbiome therapeutics have emerged as promising next-generation drug candidates, offering advantages over traditional medications. In 2022, the Food and Drug Administration approved the first microbiome therapeutic for recurrent Clostridium infections, and extensive research is underway on microbiome treatments for various challenging diseases, including metabolic disorders and cancer. Research on microbiomes concerning tuberculosis commenced roughly a decade ago, and the scope of this research has broadened considerably over the last five years, with microbiome therapeutics now viewed as viable options for managing drug-resistant tuberculosis. Nevertheless, the understanding of their mechanisms is still in its infancy. Although autophagy has been extensively studied in other diseases, research into its role in tuberculosis is just beginning, with preliminary developments in progress. Against this backdrop, this comprehensive review begins by succinctly outlining tuberculosis' characteristics and assessing existing treatments' strengths and weaknesses, followed by a detailed examination of microbiome-based therapeutic approaches for drug-resistant tuberculosis. Additionally, this review focuses on establishing a basic understanding of microbiome treatments for tuberculosis, mainly through the lens of autophagy as a mechanism of action. Ultimately, this review aims to contribute to the foundational comprehension of microbiome-based therapies for tuberculosis, thereby setting the stage for the further advancement of microbiome therapeutics for drug-resistant tuberculosis.},
}

Humans
*Autophagy
*Tuberculosis, Multidrug-Resistant/therapy/microbiology
*Microbiota
Mycobacterium tuberculosis/drug effects
Animals
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid40211685,
year = {2025},
author = {Kim, JW and Choi, EC and Lee, KJ},
title = {Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization.},
journal = {Osong public health and research perspectives},
volume = {},
number = {},
pages = {},
doi = {10.24171/j.phrp.2024.0319},
pmid = {40211685},
issn = {2210-9099},
abstract = {OBJECTIVES: This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.

METHODS: It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.

RESULTS: The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.

CONCLUSION: The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.},
}

@article {pmid40207916,
year = {2025},
author = {Lebrun-Corbin, M and Cheung, BH and Hullahalli, K and Dailey, KG and Bailey, K and Waldor, MK and Wunderink, RG and Bachta, KER and Hauser, AR},
title = {Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage.},
journal = {mBio},
volume = {},
number = {},
pages = {e0313624},
doi = {10.1128/mbio.03136-24},
pmid = {40207916},
issn = {2150-7511},
abstract = {UNLABELLED: Pseudomonas aeruginosa is a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight that P. aeruginosa gastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics of P. aeruginosa gastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose of P. aeruginosa. Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcoded P. aeruginosa library along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of the P. aeruginosa population was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the cecum expanded rapidly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage of P. aeruginosa, which may have clinical implications for hospitalized patients.

IMPORTANCE: While Pseudomonas aeruginosa is rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities. P. aeruginosa carriage is a precursor to infection. Options for treating infections caused by difficult-to-treat P. aeruginosa strains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized with P. aeruginosa in their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingested P. aeruginosa.},
}

@article {pmid40207286,
year = {2025},
author = {Ronkainen, A and Khan, I and Satokari, R},
title = {Pathogen exclusion from intestinal mucus and antimicrobial susceptibility of Bifidobacterium spp. strains from fecal donors.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {5},
pmid = {40207286},
issn = {2771-5965},
abstract = {Aim: To study the ability of bifidobacterial strains isolated from fecal donors to prevent pathogens from adhering to intestinal mucus, along with their antimicrobial susceptibility. Methods: Pathogen prevention was assessed through an in vitro adhesion assay using immobilized porcine mucus. Subsequently, bifidobacterial RNA-Seq data were analyzed to pinpoint glycoside hydrolases and glycosyltransferases possibly involved in mucus degradation affecting pathogen adhesion. The antimicrobial susceptibility of bifidobacterial strains was evaluated using in vitro susceptibility testing, followed by analysis of whole-genome sequencing data to reveal antimicrobial resistance genes. Results: Bifidobacterial strains inhibited pathogen adhesion to intestinal mucus, with most strains reducing the adhesion levels of pathogens like Escherichia coli, Listeria monocytogenes, Salmonella Typhimurium, and Staphylococcus aureus by at least 70%. None of the strains significantly affected Pseudomonas aeruginosa, but they moderately reduced the adhesion of Yersinia enterocolitica. Gene expression analysis indicated that the more effective strains expressed higher levels of glycoside hydrolases, correlating with their pathogen exclusion capabilities. Antimicrobial susceptibility testing revealed that most strains were sensitive to several antibiotics, though some exhibited resistance to tobramycin, trimethoprim, and ciprofloxacin. Notably, one strain carried the tetW gene, conferring resistance to tetracycline. Conclusion: The bifidobacterial strains characterized in this study show potential for bacteriotherapeutic applications due to their strong ability to interfere with the adhesion of pathogenic bacteria and their lack of alarming antimicrobial resistance patterns.},
}

@article {pmid40207282,
year = {2025},
author = {Stuivenberg, GA and Poon, A and Burton, JP and Spence, JD},
title = {Potential effects of probiotics on atherosclerosis.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {11},
pmid = {40207282},
issn = {2771-5965},
abstract = {The rising global incidence of atherosclerosis highlights the inadequacies in our understanding of the pathophysiology and treatment of the disease. Increasing evidence outlines the importance of the intestinal microbiome in atherosclerosis, wherein gut-derived uremic toxins (GDUTs) may be of concern. Plasma levels of the GDUTs trimethylamine n-oxide (TMAO), p-cresyl sulfate, and indoxyl sulfate are associated with accelerated renal function decline and increased cardiovascular risk. Thus, reducing the amount of GDUTs in circulation is expected to benefit patients with atherosclerosis. Because some beneficial bacteria can clear GDUTs in vitro and in vivo, orally administered probiotics targeting the intestinal tract represent a promising way to bring about these changes. Atherosclerosis such, this perspective reviews the potential use of probiotics to treat atherosclerosis, particularly in patients with non-traditional risk factors and/or impaired renal function.},
}

@article {pmid40207275,
year = {2025},
author = {Horwell, E and Bearn, P and Cutting, SM},
title = {A microbial symphony: a literature review of the factors that orchestrate the colonization dynamics of the human colonic microbiome during infancy and implications for future health.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {1},
pmid = {40207275},
issn = {2771-5965},
abstract = {Since the advent of new sequencing and bioinformatic technologies, our understanding of the human microbiome has expanded rapidly over recent years. Numerous studies have indicated causal links between alterations to the microbiome and a range of pathological conditions. Furthermore, a large body of epidemiological data is starting to suggest that exposure, or lack thereof, to specific microbial species during the first five years of life has key implications for long-term health outcomes. These include chronic inflammatory and metabolic conditions such as diabetes, asthma, inflammatory bowel disease (IBD), and obesity, with the effects lasting into adulthood. Human microbial colonisation during these first five years of life is a highly dynamic process, with multiple environmental exposures recently being characterised to have influence before the microbiome stabilises and resembles that of an adult at 3-5 years. This short period of time, known as the window of opportunity, appears to "prime" immunoregulation for later life. Understanding and appreciating this aspect of human physiology is therefore crucial for clinicians, scientists, and public health officials. This review outlines the most recent evidence for the pre- and post-natal environments that order the development of the microbiome, how these influences metabolic and immunoregulatory pathways, and their associated health outcomes. It also discusses the limitations of the current knowledge base, and describes the potential microbiome-mediated interventions and public health measures that may have therapeutic potential in the future.},
}

@article {pmid40207273,
year = {2025},
author = {van Beek, N and Katavisto, I and Lehto, M and Kolho, KL and de Vos, WM and Salonen, A and Korpela, K},
title = {Host-microbiota interactions in the infant gut revealed by daily faecal sample time series.},
journal = {Microbiome research reports},
volume = {4},
number = {1},
pages = {13},
pmid = {40207273},
issn = {2771-5965},
abstract = {Aim: This study aims to explore the interplay between host immune factors and gut microbiota in human infants in vivo using time-series daily stool samples and identify biomarkers of host-microbe interactions. Methods: 216 faecal samples collected from infants aged 5-6 or 11-12 months were analysed for gut microbiota composition, total bacterial load, and biomarkers of immune function. Results: We identified indications of microbial stimulation of eosinophil cationic protein (ECP), IgA, calprotectin (Cal), intestinal alkaline phosphatase (IAP), and Bactericidal/permeability-increasing protein (BPI) at 6 and 12 months, as well as stimulation of lipocalin 2 (LCN2), lactoferrin (LTF), and alpha-defensin-5 only at 6 months. The associations between biomarker concentrations and bacterial population growth were primarily positive at 6 months and mostly negative at 12 months, suggesting increasing host regulation of the microbiota with age. The exceptions were IAP, which was predictive of declining bacterial populations at both time points, and Cal, whose associations changed from negative at 6 months to positive at 12 months. Conclusion: There is an age-associated development in the correlation pattern between bacterial population growth and the biomarker concentrations, suggesting that host-microbe interactions change during early development. Albumin appeared as a potential marker of gut permeability, while LCN2 seemed to correlate with gut transit time. Mucin degradation appeared to decrease with age. Mucin2 and IAP emerged as potentially important regulators of the bacterial populations in the infant gut. The study demonstrates the utility of biomarker and bacteria profiling from daily stool samples for analysing in vivo associations between the immune system and the gut microbiota and provides evidence of host regulation of the microbiota in infants.},
}

@article {pmid40195307,
year = {2025},
author = {Zhang, J and Yang, J and Luo, J and Wu, W and Luo, H and Wei, W and Lyu, H and Wang, Y and Yi, H and Zhang, Y and Fan, Z and Lyu, H and Kanakaveti, VP and Qin, B and Yuan, P and Yang, R and Zhang, H and Zuo, T and Felsher, DW and Lee, MH and Li, K},
title = {Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3315},
pmid = {40195307},
issn = {2041-1723},
support = {2023A1515030245//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2023A1515010737//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 82473321//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204411//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82373139//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus acidophilus/metabolism/physiology ; *Carcinoma, Hepatocellular/therapy/microbiology ; *Liver Neoplasms/therapy/microbiology ; *Oncolytic Virotherapy/methods ; Mice ; Female ; Homeostasis ; Humans ; Oncolytic Viruses/genetics ; Mice, Inbred C57BL ; Dysbiosis/microbiology ; Cell Line, Tumor ; STAT3 Transcription Factor/metabolism ; Signal Transduction ; },
abstract = {Oncolytic viruses (OVs) hold promise for cancer treatment. However, the antitumor efficacy is limited. Microbiota plays a pivotal role in cancer treatment and its impact on oncolytic virotherapy is unknown. Here, we show that VSVΔ51 has higher antitumor efficacy for hepatocellular carcinoma in the absence of microbiota in female mouse models. VSVΔ51 infection causes microbiota dysbiosis, increasing most of the gut bacteria abundance, while decreasing the commensal Lactobacillus. VSVΔ51 reduced intestinal expression of SLC20A1 that binds to Lactobacillus acidophilus (L. acidophilus) CdpA cell wall protein through IL6-JAK-STAT3 signaling, thereby attenuating attachment and colonization of L. acidophilus. L. acidophilus supplementation confers sensitivity to VSVΔ51 through restoring gut barrier integrity and microbiota homeostasis destroyed by VSVΔ51. In this work, we show that targeting microbiota homostasis holds substantial potential in improving therapeutic outcomes of oncolytic virotherapy.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Lactobacillus acidophilus/metabolism/physiology
*Carcinoma, Hepatocellular/therapy/microbiology
*Liver Neoplasms/therapy/microbiology
*Oncolytic Virotherapy/methods
Mice
Female
Homeostasis
Humans
Oncolytic Viruses/genetics
Mice, Inbred C57BL
Dysbiosis/microbiology
Cell Line, Tumor
STAT3 Transcription Factor/metabolism
Signal Transduction

@article {pmid40193328,
year = {2025},
author = {Jagadesan, S and Guda, C},
title = {MetaDAVis: An R shiny application for metagenomic data analysis and visualization.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0319949},
doi = {10.1371/journal.pone.0319949},
pmid = {40193328},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Humans ; RNA, Ribosomal, 16S/genetics ; *Software ; *Metagenome ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {The human microbiome exerts tremendous influence on maintaining a balance between human health and disease. High-throughput sequencing has enabled the study of microbial communities at an unprecedented resolution. Generation of massive amounts of sequencing data has also presented novel challenges to analyzing and visualizing data to make biologically relevant interpretations. We have developed an interactive Metagenome Data Analysis and Visualization (MetaDAVis) tool for 16S rRNA as well as the whole genome sequencing data analysis and visualization to address these challenges using an R Shiny application. MetaDAVis can perform six different types of analyses that include: i) Taxonomic abundance distribution; ii) Alpha and beta diversity analyses; iii) Dimension reduction tasks using PCA, t-SNE, and UMAP; iv) Correlation analysis using taxa- or sample-based data; v) Heatmap generation; and vi) Differential abundance analysis. MetaDAVis creates interactive and dynamic figures and tables from multiple methods enabling users to easily understand their data using different variables. Our program is user-friendly and easily customizable allowing those without any programming background to perform comprehensive data analyses using a standalone or web-based interface.},
}

*Metagenomics/methods
Humans
RNA, Ribosomal, 16S/genetics
*Software
*Metagenome
Microbiota/genetics
High-Throughput Nucleotide Sequencing

@article {pmid40192037,
year = {2025},
author = {Verma, M and Randhawa, S and Bathla, M and Teji, N and Acharya, A},
title = {Strategic use of nanomaterials as double-edged therapeutics to control carcinogenesis via regulation of dysbiosis and bacterial infection: current status and future prospects.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4tb02409e},
pmid = {40192037},
issn = {2050-7518},
abstract = {The human microbiome plays a crucial role in modulating health and disease susceptibility through a complex network of interactions with the host. When the delicate balance of this microbial ecosystem is disrupted, it often correlates with the onset of systemic diseases. An over-abundance of pathogenic microorganisms within the microbiome has been implicated as a driving factor in the development of disease conditions such as diabetes, obesity, and chronic infections. It has been observed that microbiome dysbiosis perturbs metabolic, inflammatory, and immunological pathways, potentially facilitating carcinogenesis. Furthermore, the metabolites associated with microbial dysbiosis exert multifaceted effects, including metabolic interference, host DNA damage, and tumor promotion, further underscoring the microbiome's significance in several of the cancers. This new exploration of microbiome involvement in carcinogenesis needs additional patient sample analysis, which could provide new insights into cancer diagnosis and treatment. However, treating these diseases using drugs, traditional methods, etc. has resulted in multi-drug resistance, and this has eventually made the situation worrisome. This review highlights the importance of nanotechnology, which may tackle these pathogenic conditions simultaneously by targeting common receptors present in bacteria and cancer. Herein, we have explained how nanotechnology may come to the forefront for these treatments. It explores the potential of non-antibiotic disinfectants, i.e., nanoparticles (NPs) with dual targeting capabilities against microbes and cancer cells, using mechanisms such as ROS generation and DNA damage while minimizing the chances of drug resistance.},
}

@article {pmid40191210,
year = {2025},
author = {Karisola, P and Kanerva, M and Vuokko, A and Liira, H and Wang, S and Kvarnström, K and Varonen, M and Suojalehto, H and Alenius, H},
title = {Patients with post-COVID-19 condition show minor blood transcriptomic changes, with altered erythrocyte gene expression in a male subgroup.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1500997},
pmid = {40191210},
issn = {1664-3224},
mesh = {Humans ; *COVID-19/genetics/blood/immunology/complications ; Male ; Middle Aged ; *Transcriptome ; *SARS-CoV-2 ; Aged ; *Erythrocytes/metabolism ; Female ; Adult ; Gene Expression Profiling ; Leukocytes, Mononuclear/metabolism ; Quality of Life ; },
abstract = {BACKGROUND: The mechanisms underlying persistent symptoms after non-severe COVID-19 remain unclear. This study aimed to investigate transcriptomic changes in peripheral blood cells of patients with post-COVID-19 condition (PCC) and assess if distinct clinical subtypes with specific gene signatures could be identified.

METHODS: The cohort included 111 PCC patients from the SARS-CoV-2 Omicron variant era, with 57 recovered (Recov) and 54 having prolonged symptoms indicative of PCC. The results were compared to 63 healthy controls (Ctrl) without known SARS-CoV-2 infection. Clinical data included patient assessments, laboratory results, comorbidities, and questionnaires on quality of life and functioning. Transcriptomic analysis and cellular deconvolution methods were used on total RNA from peripheral blood mononuclear cells (PBMCs).

RESULTS: PCC patients had more comorbidities (mean 1.3) and more frequently (59%) at least one comorbidity than recovered patients (31%) and controls (24%). Overall, past COVID-19 illness or current PCC symptoms caused minimal changes in the blood cell transcriptome, with only 3-6 differentially expressed genes (DEGs) identified across comparisons. However, a subset of male PCC patients exhibited an increased fraction of deconvoluted erythroblasts and significant genome-wide gene expression changes, with 399 DEGs compared to recovered and control males. These genes were enriched in pathways related to heme metabolism and gas exchange in erythrocytes.

CONCLUSIONS: Persistent symptoms in PCC are multifactorial and not directly linked to peripheral blood cell gene expression changes. However, a subgroup of male PCC patients shows distinct erythrocyte responses that may contribute to long-term symptoms.},
}

Humans
*COVID-19/genetics/blood/immunology/complications
Male
Middle Aged
*Transcriptome
*SARS-CoV-2
Aged
*Erythrocytes/metabolism
Female
Adult
Gene Expression Profiling
Leukocytes, Mononuclear/metabolism
Quality of Life

@article {pmid40190580,
year = {2025},
author = {Delicati, A and Marcante, B and Catelan, D and Biggeri, A and Caenazzo, L and Tozzo, P},
title = {Hand-to-surface bacterial transfer and healthcare-associated infections prevention: a pilot study on skin microbiome in a molecular biology laboratory.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1546298},
pmid = {40190580},
issn = {2296-858X},
abstract = {BACKGROUND: Healthcare-associated infections (HAIs) are a major global public health problem, contributing significantly to patient morbidity and mortality. This study analyses differences in type and amounts of bacteria transferred from volunteers' dominant palm to two healthcare-relevant surfaces (glass and laminate table), both before and after hand washing with water and antibacterial soap. The aim was to understand hand-to-surface microbial contamination and support the development of HAI prevention strategies.

METHODS: Microbial DNA was extracted and sequenced to identify bacteria species. Taxonomic and statistical analyses were performed to evaluate bacterial diversity and abundance across the experimental groups.

RESULTS: The results confirmed greater bacteria abundance and species richness on palm compared to surfaces, with a significant reduction after hand washing, especially on glass. Taxa analysis highlighted the increased persistence of Gram-negative HAIs-related bacteria on laminate surface, while Gram-positive opportunistic bacteria were more abundant on palms and glass surface. Beta diversity confirmed significant differences in microbial composition between the groups, highlighting the importance of bacteria-surface characteristics in designing preventive measures.

CONCLUSION: Despite some limitations, our study emphasizes the importance of microbiological surveillance for all opportunistic bacteria with pathogenic potential. These findings can contribute to more effective guidelines for surface disinfection and hand washing, key elements in preventing HAIs.},
}

@article {pmid40188410,
year = {2025},
author = {Oyovwi, MO and Ben-Azu, B and Babawale, KH},
title = {Therapeutic potential of microbiome modulation in reproductive cancers.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {5},
pages = {152},
pmid = {40188410},
issn = {1559-131X},
mesh = {Humans ; *Microbiota ; Probiotics/therapeutic use ; Female ; Dysbiosis/microbiology/therapy ; *Genital Neoplasms, Female/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Animals ; Gastrointestinal Microbiome ; },
abstract = {The human microbiome, a complex ecosystem of microbial communities, plays a crucial role in physiological processes, and emerging research indicates a potential link between it and reproductive cancers. This connection highlights the significance of understanding the microbiome's influence on cancer development and treatment. A comprehensive review of current literature was conducted, focusing on studies that investigate the relationship between microbiome composition, reproductive cancer progression, and potential therapeutic approaches to modulate the microbiome. Evidence suggests that imbalances in the microbiome, known as dysbiosis, may contribute to the development and progression of reproductive cancers. Specific microbial populations have been associated with inflammatory responses, immune modulation, and even resistance to conventional therapies. Interventions such as probiotics, dietary modifications, and fecal microbiota transplantation have shown promise in restoring healthy microbiome function and improving cancer outcomes in pre-clinical models, with pilot studies in humans indicating potential benefits. This review explores the therapeutic potential of microbiome modulation in the management of reproductive cancers, discussing the mechanisms involved and the evidence supporting microbiome-targeted therapies. Future research is warranted to unravel the complex interactions between the microbiome and reproductive cancer pathophysiology, paving the way for innovative approaches.},
}

Humans
*Microbiota
Probiotics/therapeutic use
Female
Dysbiosis/microbiology/therapy
*Genital Neoplasms, Female/microbiology/therapy
Fecal Microbiota Transplantation/methods
Animals
Gastrointestinal Microbiome

@article {pmid40177558,
year = {2025},
author = {Xia, S and Jiang, D and Zhou, Q and Lyu, H and Voigt, AY and Zhou, X and Zhou, Z and Huang, Y},
title = {Unlocking the healthy human microbiome: Redefining core microbial signatures.},
journal = {Acta pharmaceutica Sinica. B},
volume = {15},
number = {2},
pages = {1189-1192},
doi = {10.1016/j.apsb.2025.01.001},
pmid = {40177558},
issn = {2211-3835},
}

@article {pmid40174574,
year = {2025},
author = {Zeng, S and Almeida, A and Mu, D and Wang, S},
title = {Embracing the unknown: Proteomic insights into the human microbiome.},
journal = {Cell metabolism},
volume = {37},
number = {4},
pages = {799-801},
doi = {10.1016/j.cmet.2025.02.003},
pmid = {40174574},
issn = {1932-7420},
abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.},
}

@article {pmid40170399,
year = {2025},
author = {Schütz, B and Krause, FF and Taudte, RV and Zaiss, MM and Luu, M and Visekruna, A},
title = {Modulation of Host Immunity by Microbiome-Derived Indole-3-Propionic Acid and Other Bacterial Metabolites.},
journal = {European journal of immunology},
volume = {55},
number = {4},
pages = {e202451594},
doi = {10.1002/eji.202451594},
pmid = {40170399},
issn = {1521-4141},
support = {VI562/7-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Indoles/immunology ; Animals ; Immunity, Mucosal/immunology ; Dysbiosis/immunology ; Bacteria/immunology/metabolism ; Propionates ; },
abstract = {In recent years, we have witnessed a rapidly growing interest in the intricate communications between intestinal microorganisms and the host immune system. Research on the human microbiome is evolving from merely descriptive and correlative studies to a deeper mechanistic understanding of the bidirectional interactions between gut microbiota and the mucosal immune system. Despite numerous challenges, it has become increasingly evident that an imbalance in gut microbiota composition, known as dysbiosis, is associated with the development and progression of various metabolic, immune, cancer, and neurodegenerative disorders. A growing body of evidence highlights the importance of small molecules produced by intestinal commensal bacteria, collectively referred to as gut microbial metabolites. These metabolites serve as crucial diffusible messengers, translating the microbial language to host cells. This review aims to explore the complex and not yet fully understood molecular mechanisms through which microbiota-derived metabolites influence the activity of the immune cells and shape immune reactions in the gut and other organs. Specifically, we will discuss recent research that reveals the close relationship between microbial indole-3-propionic acid (IPA) and mucosal immunity. Furthermore, we will emphasize the beneficial effects of IPA on intestinal inflammation and discuss its potential clinical implications.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Indoles/immunology
Animals
Immunity, Mucosal/immunology
Dysbiosis/immunology
Bacteria/immunology/metabolism
Propionates

@article {pmid40166311,
year = {2025},
author = {Inglis, LK and Grigson, SR and Roach, MJ and Edwards, RA},
title = {Prophages as a source of antimicrobial resistance genes in the human microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.19.644263},
pmid = {40166311},
issn = {2692-8205},
abstract = {UNLABELLED: Prophages-viruses that integrate into bacterial genomes-are ubiquitous in the microbial realm. Prophages contribute significantly to horizontal gene transfer, including the potential spread of antimicrobial resistance (AMR) genes, because they can collect host genes. Understanding their role in the human microbiome is essential for fully understanding AMR dynamics and possible clinical implications. We analysed almost 15,000 bacterial genomes for prophages and AMR genes. The bacteria were isolated from diverse human body sites and geographical regions, and their genomes were retrieved from GenBank. AMR genes were detected in 6.6% of bacterial genomes, with a higher prevalence in people with symptomatic diseases. We found a wide variety of AMR genes combating multiple drug classes. We discovered AMR genes previously associated with plasmids, such as blaOXA-23 in Acinetobacter baumannii prophages or genes found in prophages in species they had not been previously described in, such as mefA-msrD in Gardnerella prophages, suggesting prophage-mediated gene transfer of AMR genes. Prophages encoding AMR genes were found at varying frequencies across body sites and geographical regions, with Asia showing the highest diversity of AMR genes.

IMPORTANCE: Antimicrobial resistance (AMR) is a growing threat to public health, and understanding how resistance genes spread between bacteria is essential for controlling their dissemination. Bacteriophages, viruses that infect bacteria, have been recognised as potential vehicles for transferring these resistance genes, but their role in the human microbiome remains poorly understood. We examined nearly 15,000 bacterial genomes from various human body sites and regions worldwide to investigate how often prophages carry AMR genes in the human microbiome. Although AMR genes were uncommon in prophages, we identified diverse resistance genes across multiple bacterial species and drug classes, including some typically associated with plasmids. These findings reveal that prophages may contribute to the spread of resistance genes, highlighting an overlooked mechanism in the dynamics of AMR transmission. Ongoing monitoring of prophages is critical to fully understanding the pathways through which resistance genes move within microbial communities and impact human health.},
}

@article {pmid40166302,
year = {2025},
author = {Walker, AR and Pham, DN and Noeparvar, P and Peterson, AM and Lipp, MK and Lemos, JA and Zeng, L},
title = {FRUCTOSE ACTIVATES A STRESS RESPONSE SHARED BY METHYLGLYOXAL AND HYDROGEN PEROXIDE IN STREPTOCOCCUS MUTANS.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.26.620100},
pmid = {40166302},
issn = {2692-8205},
abstract = {Fructose catabolism by Streptococcus mutans is initiated by three PTS transporters yielding either fructose-1-phoshate (F-1-P) or fructose-6-phosphate (F-6-P). Deletion of one such F-1-P-generating PTS, fruI, has been shown to reduce the cariogenicity of S. mutans in rats fed a high-sucrose diet. Moreover, a recent study linked fructose metabolism in S. mutans to a reactive electrophile species (RES) methylglyoxal. Here, we conducted a comparative transcriptomic analysis of exponentially grown S. mutans shocked with 50 mM fructose, 50 mM glucose, 5 mM methylglyoxal, or 0.5 mM hydrogen peroxide (H2O2). The results revealed a striking overlap between the fructose and methylglyoxal transcriptomes, totaling 176 genes, 61 of which were also shared with the H2O2 transcriptome. This core of 61 genes encompassed many of the same pathways affected by exposure to low pH or zinc intoxication. Consistent with these findings, fructose negatively impacted metal homeostasis of a mutant deficient in zinc expulsion and the growth of a mutant of the major oxidative stress regulator SpxA1. We further demonstrated the induction of the superoxide dismutase (sodA) and the fruRKI operon by different levels of fructose. Finally, fructose metabolism lowered culture pH at a faster pace, allowed better survival under acidic and nutrient-depleted conditions, and enhanced the competitiveness of S. mutans against Streptococcus sanguinis, although a moderated level of F-1-P might further boost some of these benefits. In conclusion, fructose metabolism is integrated into the stress core of S. mutans and regulates critical functions required for survival in both the oral cavity and during systemic infections. Importance. Fructose is a common monosaccharide in the biosphere, yet its overconsumption has been linked to various health problems in humans including insulin resistance, obesity, diabetes, and non-alcoholic liver diseases. These effects are in large part attributed to the unique biochemical characteristics and metabolic responses associated with the degradation of fructose. Yet, an understanding of the effects of fructose on the physiology of bacteria and its implications to the human microbiome is severely lacking. Here we performed a series of analyses on the gene regulation of a dental pathogen Streptococcus mutans by exposing it to fructose and other important stress agents. Further supported by growth, persistence, and competition assays, our findings revealed the ability of fructose to activate a set of cellular functions that may prove critical to the ability of the bacterium to persist and cause diseases both within and without of the oral cavity.},
}

@article {pmid40162761,
year = {2025},
author = {Jung, M and Boutin, S and Simon, MM and Frese, C},
title = {Comparative analysis of oral microbiome in molar-incisor-hypomineralization vs healthy age-matched controls.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0289724},
doi = {10.1128/spectrum.02897-24},
pmid = {40162761},
issn = {2165-0497},
abstract = {UNLABELLED: Molar-incisor-hypomineralization (MIH) is one of the most challenging dental diseases in children. While the association of oral microbiomes with caries and periodontitis has been studied thoroughly, limited data on the microbial composition in MIH and its clinical significance exist. This cross-sectional study aimed to compare the supragingival plaque microbiome between children and adolescents affected by MIH and a healthy age-matched control group. Ninety-five patients aged 7-17 years were recruited at the Department of Conservative Dentistry, Heidelberg University Hospital. The final sample included 29 participants with a confirmed diagnosis of MIH, treated preventively and restoratively, and 35 orally healthy controls. Clinical data were obtained, and supragingival plaque samples were collected using OMNIgene ORAL OMR-110 (DNA Genotek Inc.), followed by 16S rRNA amplicon sequencing. The microbiome composition was analyzed using α-diversity (Shannon index) and evenness (Pielou index), with group differences assessed using permutational multivariate analysis of variance (PERMANOVA) and MaAsLin2. The overall microbiome composition showed mostly similarities between both groups (PERMANOVA: R[2] = 0.019, P-value = 0.287), indicating no major dysbiosis. However, a significant decrease in α-diversity and evenness was observed with an increasing number of MIH-affected teeth. Pronounced positive correlations were found between ASV0055 (Streptococcus spp.), caries experience, and MIH severity. ASV0100 (Mannheimia sp.) increased significantly with the increasing number of MIH-affected teeth, whereas ASV0053 (Bergeyella sp.) decreased with higher caries experience. In summary, the oral microbiome of children and adolescents with MIH exhibits no significant differences from healthy children and adolescents of the same age group. Depending on MIH severity, the presence of early plaque-forming species and cariogenic biofilm may increase, requiring intensive, tailored preventive care and appropriate restorative treatment to achieve microbial homeostasis.

IMPORTANCE: Molar-incisor-hypomineralization (MIH) represents a significant burden for affected children and adolescents, playing an increasingly important role in pediatric dentistry worldwide. Despite its high global prevalence, data on the microbiome of MIH patients remains limited. This study is the first to compare the oral microbiome composition of MIH patients with a healthy control group, making a significant contribution to pediatric dentistry and microbiology. Our results indicate that the oral microbiome of children with MIH is similar to that of healthy children of the same age. Although this structural anomaly predisposes patients to caries, effective preventive and restorative treatments can help maintain microbial homeostasis. However, MIH-affected children remain high-risk patients, as the disease severity may reduce microbial diversity. Furthermore, the increased abundance of Streptococcus spp. in MIH patients indicates a higher caries susceptibility, emphasizing the need for targeted dental care focusing on plaque control and topical fluoride use.},
}

@article {pmid40161742,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.11.642547},
pmid = {40161742},
issn = {2692-8205},
abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.

IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}

@article {pmid40158322,
year = {2025},
author = {Hamza, M and Wang, S and Liu, Y and Li, K and Zhu, M and Chen, L},
title = {Unraveling the potential of bioengineered microbiome-based strategies to enhance cancer immunotherapy.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128156},
doi = {10.1016/j.micres.2025.128156},
pmid = {40158322},
issn = {1618-0623},
abstract = {The human microbiome plays a pivotal role in the field of cancer immunotherapy. The microbial communities that inhabit the gastrointestinal tract, as well as the bacterial populations within tumors, have been identified as key modulators of therapeutic outcomes, affecting immune responses and reprogramming the tumor microenvironment. Advances in synthetic biology have made it possible to reprogram and engineer these microorganisms to improve antitumor activity, enhance T-cell function, and enable targeted delivery of therapies to neoplasms. This review discusses the role of the microbiome in modulating both innate and adaptive immune mechanisms-ranging from the initiation of cytokine production and antigen presentation to the regulation of immune checkpoints-and discusses how these mechanisms improve the efficacy of immune checkpoint inhibitors. We highlight significant advances with bioengineered strains like Escherichia coli Nissle 1917, Lactococcus lactis, Bifidobacterium, and Bacteroides, which have shown promising antitumor efficacy in preclinical models. These engineered microorganisms not only efficiently colonize tumor tissues but also help overcome resistance to standard therapies by reprogramming the local immune environment. Nevertheless, several challenges remain, such as the requirement for genetic stability, effective tumor colonization, and the control of potential safety issues. In the future, the ongoing development of genetic engineering tools and the optimization of bacterial delivery systems are crucial for the translation of microbiome-based therapies into the clinic. This review highlights the potential of bioengineered microbiota as an innovative, personalized approach in cancer immunotherapy, bringing hope for more effective and personalized treatment options for patients with advanced malignancies.},
}

@article {pmid40158141,
year = {2025},
author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY},
title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {87},
pmid = {40158141},
issn = {2049-2618},
support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; },
mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; },
abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.},
}

Humans
*Neural Networks, Computer
*Microbiota
Metagenomics/methods
Bacteria/classification/genetics
Computer Simulation

@article {pmid40156096,
year = {2025},
author = {Patjas, A and Kantele, A},
title = {Travel to low- and middle-income countries and travellers' diarrhoea increase risk of mismatching antimicrobial therapy for urinary tract infection.},
journal = {Journal of travel medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/jtm/taaf025},
pmid = {40156096},
issn = {1708-8305},
abstract = {BACKGROUND: Travel to low- and middle-income countries (LMICs) increases the risk of urinary tract infections (UTIs), including those caused by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE). Focusing on international travel, we explored resistance profiles of urinary ESBL-PE and non-ESBL-PE isolates in a low antimicrobial resistance prevalence country and factors associated with UTI treatment failure.

METHODS: During 2015-19, we recruited 18-65-year-old individuals with recent ESBL-PE UTI and a respective cohort of those with non-ESBL-PE UTI to complete questionnaires on symptoms, antibiotic therapies, and treatment failure risk factors. We compared uropathogens' resistance profiles among patients with or without LMIC travel history and conducted multivariable analyses to identify factors contributing to mismatching antimicrobial treatment (uropathogen resistant to the initial antimicrobial used) and clinical failure.

RESULTS: Among non-ESBL-PE UTI patients (n = 187), trimethoprim resistance was more common in isolates from individuals with recent LMIC travel (8/19, 42.1%) compared to those without (30/167, 18.0%) (OR 3.3, CI95% 1.2-9.0). ESBL-PE isolates (n = 130) showed no differences in resistance profiles with respect to LMIC travel history.In the group non-ESBL-PE UTI, risk factors included microbiological mismatching recent LMIC travel (AOR 3.6, CI95% 1.0-12.7) and travellers' diarrhoea (AOR 7.1, CI95% 1.1-45.6); no factors were significantly associated with mismatching in the group ESBL-PE UTI. As risk factors for clinical failure, in the group non-ESBL-PE UTI, we identified microbiological mismatching (AOR 15.2, CI95% 4.0-57.9), and renal/bladder disease (AOR 5.2, CI95% 1.1-23.2), and in the group ESBL-PE UTI, microbiological mismatching (AOR 8.1, CI95% 2.6-24.7).

CONCLUSIONS: LMIC travel increases the risk of nonmatching empiric antimicrobials, concurring with increased trimethoprim resistance rates among the non-ESBL-PE isolates. Our data suggest that UTI patients with recent LMIC travel should not be empirically treated with trimethoprim and, when possible, urinary culturing is warranted.},
}

@article {pmid40155374,
year = {2025},
author = {Zhang, J and Zhang, D and Xu, Y and Zhang, J and Liu, R and Gao, Y and Shi, Y and Cai, P and Zhong, Z and He, B and Li, X and Zhou, H and Chen, M and Li, YX},
title = {Large-scale biosynthetic analysis of human microbiomes reveals diverse protective ribosomal peptides.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3054},
pmid = {40155374},
issn = {2041-1723},
support = {C7014-24GF//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Peptides/metabolism/chemistry ; *Microbiota ; *Ribosomes/metabolism ; *Protein Processing, Post-Translational ; Biofilms ; Inflammatory Bowel Diseases/microbiology ; Biological Products/metabolism ; Genome, Bacterial ; Mice, Inbred C57BL ; Ribosomal Proteins/metabolism/genetics ; },
abstract = {The human microbiome produces diverse metabolites that influence host health, yet the chemical landscape of ribosomally synthesized and post-translationally modified peptides (RiPPs)-a versatile class of bioactive compounds-remains underexplored. Here, we conduct a large-scale biosynthetic analysis of 306,481 microbial genomes from human-associated microbiomes, uncovering a broad array of yet-to-be-discovered RiPPs. These RiPPs are distributed across various body sites but show a specific enrichment in the gut and oral microbiome. Big data omics analysis reveals that numerous RiPP families are inversely related to various diseases, suggesting their potential protective effects on health. For a proof of principle study, we apply the synthetic-bioinformatic natural product (syn-BNP) approach to RiPPs and chemically synthesize nine autoinducing peptides (AIPs) for in vitro and ex vivo assay. Our findings reveal that five AIPs effectively inhibit the biofilm formation of disease-associated pathogens. Furthermore, when ex vivo testing gut microbiota from mice with inflammatory bowel disease, we observe that two AIPs can regulate the microbial community and reduce harmful species. These findings highlight the vast potential of human microbial RiPPs in regulating microbial communities and maintaining human health, emphasizing their potential for therapeutic development.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome
*Peptides/metabolism/chemistry
*Microbiota
*Ribosomes/metabolism
*Protein Processing, Post-Translational
Biofilms
Inflammatory Bowel Diseases/microbiology
Biological Products/metabolism
Genome, Bacterial
Mice, Inbred C57BL
Ribosomal Proteins/metabolism/genetics

@article {pmid40144639,
year = {2025},
author = {Sabu, P and Pathak, HB and Nissen, E and Chalise, P and Koestler, DC and Godwin, AK and Umar, S and Spoozak, L and Jewell, A and Mahoney, DE},
title = {Translational Implications of The Gut Microbiome in Women with A Benign or Malignant Pelvic Mass.},
journal = {Annals of obstetrics and gynecology},
volume = {8},
number = {1},
pages = {},
pmid = {40144639},
issn = {2641-6522},
abstract = {OBJECTIVE: The role of the gut microbiome in non-gastrointestinal cancers has generated growing interest in the field of gynecologic oncology. Our objective was to characterize the gut microbiome in women with a pelvic mass suspicious for ovarian cancer. We hypothesized that (1) women with a pelvic mass would have reduced gut microbiota bacterial diversity compared to healthy controls and (2) gut microbial diversity would differ between benign disease compared to ovarian cancer.

METHODS: In this case-control observational study, patients who presented with a suspicious pelvic mass were recruited from university affiliated gynecologic oncology clinics for fecal biospecimen donation. Fecal samples that were obtained from patients underwent 16S rRNA gene sequencing for microbial evaluation and statistical analysis. We used the Human Microbiome Project (HMP) Data Portal to compare gut microbiota profiles for our study to that of healthy female controls.

RESULTS: Fifteen patients with a pelvic mass were included ages 24-75 years. When comparing the gut microbiomes of these patients to 82 healthy females from the HMP Dataset, those with a pelvic mass had a significantly lower microbiota gut bacterial diversity. On the final pathology, 8 of the 15 patients with a suspicious pelvic mass had ovarian cancer and 7 had benign disease. Although not statistically significant, the alpha diversity was marginally reduced in patients with ovarian cancer compared to those with benign disease.

CONCLUSION: These findings underscore the necessity for validation in larger patient cohorts for clinical translation as a potential tool for disease diagnostics and disease prediction in diverse populations.},
}

@article {pmid40142442,
year = {2025},
author = {Fan, X and Lv, N and Quan, Z},
title = {Culturable Human Microorganisms and the Impact of Transportation Conditions on Cultivability.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030549},
pmid = {40142442},
issn = {2076-2607},
support = {2021YFA1301000//the National Key Research and Development Program of China/ ; 2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 32470099//the National Natural Foundation of China/ ; },
abstract = {The composition of the human microbiome is a critical health indicator, and culture-independent methodologies have substantially advanced our understanding of human-associated microorganisms. However, precise identification and characterization of microbial strains require culture-based techniques. Recently, the resurgence of culturomics, combined with high-throughput sequencing technology, has reduced the high labor demand of pure culture methods, facilitating a more efficient and comprehensive acquisition of culturable microbial strains. This study employed an integrated approach combining culturomic and high-throughput sequencing to identify culturable microorganisms on the human scalp and in human saliva and feces. Several Staphylococcus strains were identified from the scalp, whereas anaerobic microorganisms were dominant in the saliva and fecal samples. Additionally, the study highlighted the beneficial effects of transportation conditions (liquid nitrogen treatment, dry ice transport, and dimethyl sulfoxide [DMSO] buffer) in preserving culturable microorganisms. A robust methodology was developed for the large-scale acquisition of culturable microorganisms with optimized transport conditions that enhance the potential for isolating a greater diversity of culturable strains.},
}

@article {pmid40140901,
year = {2025},
author = {Wu, Y and Cheng, R and Lin, H and Li, L and Jia, Y and Philips, A and Zuo, T and Zhang, H},
title = {Gut virome and its implications in the pathogenesis and therapeutics of inflammatory bowel disease.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {183},
pmid = {40140901},
issn = {1741-7015},
support = {2023YFS0279//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; },
abstract = {Inflammatory bowel disease (IBD) refers to chronic, recurrent inflammatory intestinal disorders, primarily including Crohn's disease (CD) and Ulcerative colitis (UC). Numerous studies have elucidated the importance of the gut microbiome in IBD. Recently, numerous studies have focused on the gut virome, an intriguing and enigmatic aspect of the gut microbiome. Alterations in the composition of phages, eukaryotic viruses, and human endogenous retroviruses that occur in IBD suggest potential involvement of the gut virome in IBD. Nevertheless, the mechanisms by which it maintains intestinal homeostasis and interacts with diseases are only beginning to be understood. Here, we thoroughly reviewed the composition of the gut virome in both healthy individuals and IBD patients, emphasizing the key viruses implicated in the onset and progression of IBD. Furthermore, the complex connections between the gut virome and the intestinal barrier, immunity, and gut microbiome were dissected to advance the interpretation of IBD pathogenesis. The updated discussion of the evidence regarding the gut virome will advance our knowledge in gut virome and chronic gastrointestinal diseases. Targeting the gut virome is a promising avenue for IBD treatment in future.},
}

Humans
*Inflammatory Bowel Diseases/therapy/microbiology/virology
*Virome
*Gastrointestinal Microbiome

@article {pmid40140341,
year = {2025},
author = {Rodolfi, S and Selmi, C},
title = {Environmental factors and rheumatic diseases.},
journal = {Best practice & research. Clinical rheumatology},
volume = {},
number = {},
pages = {102053},
doi = {10.1016/j.berh.2025.102053},
pmid = {40140341},
issn = {1532-1770},
abstract = {The pathogenesis and pathophysiology of rheumatic diseases is complex and relies on the interaction of different factors. The common view is that the pathological autoimmunity develops in genetically predisposed individuals upon exposure to an environmental trigger. This highlights the importance of recognizing and deconstructing the effects of environmental agents in rheumatic diseases. Several factors have been identified in the last decades, with detrimental or protective effects, impacting not only on disease onset, but also on its natural history. Cigarette smoking has been identified as one of the strongest environmental risk factors, being associated with disease development and severity for several rheumatic diseases, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and spondyloarthropathies. Moreover, other airborne pollutants, such as silica, solvents, asbestos and metals are recognized risk factors for rheumatic diseases. The effect of some other agents is however not straightforward, of which a remarkable example is alcohol consumption. Alcohol has been associated with both pro- and anti-inflammatory effects, exerting a variable effect on rheumatic diseases depending on quantity and frequency of consumption, as well as sex and ethnicity. Similarly, ultraviolet light exposure has been associated with a higher risk of SLE but lower risk of RA. The relationship between microbial exposure and autoimmunity is also complex: while some infectious agents increase the risk of rheumatic diseases, it is widely accepted that less exposure to microbial agents, particularly during immune system development, increases the risk of autoimmunity. Furthermore, in recent years the spotlight has switched to the human microbiome, as alterations in organ-specific microbiome composition are anticipated to be early participants in the onset of immune-mediated illnesses. The aim of this review is to highlight the most relevant environmental factors and their role in Rheumatology, with a specific focus on proposed pathophysiological effect and correlation with clinical outcomes.},
}

@article {pmid40137778,
year = {2025},
author = {Papamentzelopoulou, M and Pitiriga, VC},
title = {Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030293},
pmid = {40137778},
issn = {2076-0817},
mesh = {Humans ; *Papillomavirus Infections/immunology/virology ; *Microbiota/physiology ; Female ; Papillomaviridae/genetics ; Uterine Cervical Neoplasms/virology/immunology/microbiology ; Dysbiosis/immunology ; },
abstract = {The human microbiome plays a vital role in maintaining human homeostasis, acting as a key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption of the symbiotic relationship between the host and the local microbiota, leading to the pathogenesis of various diseases, including viral infections and cancers. One of the most common infectious agents causing cancer is the human papilloma virus (HPV), which accounts for more than 90% of cervical cancers. In most cases, the host immune system is activated and clears HPV, whereas in some cases, the infection persists and can lead to precancerous lesions. Over the last two decades, the advent of next-generation sequencing (NGS) technology and bioinformatics has allowed a thorough and in-depth analysis of the microbial composition in various anatomical niches, allowing researchers to unveil the interactions and the underlying mechanisms through which the human microbiota could affect HPV infection establishment, persistence, and progression. Accordingly, the present narrative review aims to shed light on our understanding of the role of the human microbiome in the context of HPV infection and its progression, mainly to cervical cancer. Furthermore, we explore the mechanisms by which the composition and balance of microbial communities exert potential pathogenic or protective effects, leading to either HPV persistence and disease outcomes or clearance. Special interest is given to how the microbiome can modulate host immunity to HPV infection. Lastly, we summarize the latest findings on the therapeutic efficacy of probiotics and prebiotics in preventing and/or treating HPV infections and the potential of vaginal microbiota transplantation while highlighting the significance of personalized medicine approaches emerging from NGS-based microbiome profiling and artificial intelligence (AI) for the optimal management of HPV-related diseases.},
}

Humans
*Papillomavirus Infections/immunology/virology
*Microbiota/physiology
Female
Papillomaviridae/genetics
Uterine Cervical Neoplasms/virology/immunology/microbiology
Dysbiosis/immunology

@article {pmid40137432,
year = {2025},
author = {Ziogou, A and Giannakodimos, I and Giannakodimos, A and Mitakidi, E and Charalampakis, N and Ioannou, P},
title = {Primary Actinomycosis of the Stomach: A Review of the Literature for A Rare Entity.},
journal = {Journal of personalized medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jpm15030116},
pmid = {40137432},
issn = {2075-4426},
abstract = {Background/Objectives: Primary gastric actinomycosis is extremely rare and only a limited number of cases are published in the literature. Actinomycosis is caused by anaerobic Gram-positive bacteria; these microorganisms are members of the normal human microbiome and occasionally lead to infection, especially in immunocompromised patients or patients subjected to abdominal surgery. Advances in personalized medicine, including tailored antimicrobial therapy based on individual patient profiles, may enhance treatment efficacy and reduce unnecessary interventions. Methods: A review was performed through a literature search of the PubMed/MedLine and Scopus databases. Results: A total of 27 patients were included, 15 males (55.56%) and 12 (44.44%) females, with a mean age of 55.11 ± 17.48 years. Among the included patients, 25.93% had a history of abdominal surgery. Abdominal pain (73.08%), weight loss (40.74%), nausea or vomiting (30.77%) and fever (19.23%) constitute the most commonly reported clinical manifestations. Endoscopy (59.26%), computed tomography (48.15%), ultrasonography (22.22%) and magnetic resonance imaging (11.11%) assisted in indicating the primary lesion. Diagnosis was achieved preoperatively in 66.66% of patients, via endoscopy and biopsy (51.85%) or via cultures (14.81%), while nine cases (33.33%) were diagnosed postoperatively. The therapeutic approaches included antimicrobial administration (32%), surgery (24%) or both (44%). The most widely used antimicrobial was penicillin (77.78%) and the mean duration of antimicrobial treatment was 5.85 months. The protocol for this review was registered in Prospero (ID:CRD42025649532). Conclusions: Due to the divergent clinical presentation of primary gastric actinomycosis, clinicians should be aware of this rare entity in order to establish diagnosis in a timely manner and provide prompt and effective treatment.},
}

@article {pmid40128848,
year = {2025},
author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC},
title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {81},
pmid = {40128848},
issn = {2049-2618},
support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; },
abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.

RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Feces/microbiology
*Bacteria/genetics/classification/metabolism
Mice
Animals
Epigenesis, Genetic
Epigenome
Female
Male
Phosphates/metabolism

@article {pmid40122597,
year = {2025},
author = {Su, R and Wen, W and Jin, Y and Cao, Z and Feng, Z and Chen, J and Lu, Y and Zhou, G and Dong, C and Gao, S and Li, X and Zhang, H and Chao, K and Lan, P and Wu, X and Philips, A and Li, K and Gao, X and Zhang, F and Zuo, T},
title = {Dietary whey protein protects against Crohn's disease by orchestrating cross-kingdom interaction between the gut phageome and bacteriome.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334516},
pmid = {40122597},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiome and diet are important factors in the pathogenesis and management of Crohn's disease (CD). However, the role of the gut phageome under dietary influences is unknown.

OBJECTIVE: We aim to explore the effect of diet on the gut phageome-bacteriome interaction linking to CD protection.

DESIGN: We recruited CD patients and healthy subjects (n=140) and conducted a multiomics investigation, including paired ileal mucosa phageome and bacteriome profiling, dietary survey and phenome interrogation. We screened for the effect of diet on the gut phageome and bacteriome, as well as its epidemiological association with CD risks. The underlying mechanisms were explored in target phage-bacteria monocultures and cocultures in vitro and in two mouse models in vivo.

RESULTS: On dietary screening in humans, whey protein (WP) consumption was found to profoundly impact the gut phageome and bacteriome (more pronounced on the phageome) and was associated with a lower CD risk. Indeed, the WP reshaped gut phageome can causally attenuate intestinal inflammation, as shown by faecal phageome versus bacteriome transplantation from WP-consuming versus WP-non-consuming mice to recipient mice. Mechanistically, WP induced phage (a newly isolated phage AkkZT003P herein) lysis of the mucin-foraging bacterium Akkermansia muciniphila, which unleashed the symbiotic bacterium Streptococcus thermophilus to counteract intestinal inflammation.

CONCLUSION: Our study charted the importance of cross-kingdom interaction between gut phage and bacteria in mediating the dietary effect on CD protection. Importantly, we uncovered a beneficial dietary WP, a keystone phage AkkZT003P, and a probiotic S. thermophilus that can be used in CD management in the future.},
}

@article {pmid40120775,
year = {2025},
author = {Onali, T and Slabá, H and Jian, C and Koivumäki, T and Päivärinta, E and Marttinen, M and Määttänen, M and Salonen, A and Pajari, AM},
title = {Berry supplementation in healthy volunteers modulates gut microbiota, increases fecal polyphenol metabolites and reduces viability of colon cancer cells exposed to fecal water- a randomized controlled trial.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109906},
doi = {10.1016/j.jnutbio.2025.109906},
pmid = {40120775},
issn = {1873-4847},
abstract = {SCOPE: Diets high in red and processed meat and low in plant-based foods are associated with an increased risk of colorectal cancer. We investigated whether berry supplementation can impact gut metabolism to counteract the presumably cancer promoting luminal environment sustained by high red and processed meat consumption.

METHODS AND RESULTS: Altogether 43 healthy adults were randomized either into Meat group (150 g/d red and processed pork meat) or Meat & Berries group (150 g/d red and processed meat and 200 g/d of mixed berries). Fecal samples and 3-day food records were collected at baseline and at the end of the four-week intervention. Intakes of vitamin C, vitamin E, manganese, insoluble fibre, and the polyphenols available in the database were significantly higher in the Meat & Berries than Meat group. While between-group comparisons found no significant differences in the gut microbiota, the within-group analyses showed that the relative abundances of beneficial Roseburia and Faecalibacterium were decreased and an unclassified group of Peptostreptococcaceae increased significantly in the Meat group. In comparison to the Meat group, berry consumption resulted in higher fecal concentrations of p-coumaric and protocatechuic acids and lower viability of fecal water (FW) -treated CV1-P fibroblastoma and human colon adenocarcinoma HCA-7 and Caco-2 cells (P<0.05 with 30% FW).

CONCLUSIONS: Berry consumption provided protective nutrients and mitigated potentially unfavourable gut microbiota changes seen in the Meat group, increased fecal polyphenol metabolites, and reduced viability of FW-treated colon adenocarcinoma cells, collectively suggesting that berries may protect against colorectal cancer development.},
}

@article {pmid40120687,
year = {2025},
author = {Caffrey, EB and Perelman, D and Ward, CP and Sonnenburg, ED and Gardner, CD and Sonnenburg, JL},
title = {Unpacking food fermentation: Clinically relevant tools for fermented food identification and consumption.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100412},
doi = {10.1016/j.advnut.2025.100412},
pmid = {40120687},
issn = {2156-5376},
abstract = {Fermented foods have been consumed for millennia, valued for their extended shelf life, distinctive sensory properties, and potential health benefits. Emerging research suggests that fermented food consumption may contribute to gut microbiome diversity, immune modulation, and metabolic regulation; however, mechanistic insights and clinical validation remain limited. This review synthesizes current scientific evidence on the microbial and metabolite composition of fermented foods, their proposed health effects, and safety considerations for vulnerable populations. Additionally, we highlight the need for standardized definitions, serving sizes, and regulatory frameworks to enhance consumer transparency and research reproducibility. By providing a structured overview of existing data and knowledge gaps, this review establishes a foundation for integrating fermented foods into dietary recommendations and guiding future research directions. STATEMENT OF SIGNIFICANCE: While fermented foods have demonstrated benefits to human health, the gap between scientific research and marketing claims, including lack of regulatory standards in labeling can be disorienting to consumers seeking these potential benefits. This review provides an updated perspective on the role of fermented foods in health, emphasizing clinically relevant tools, research opportunities, and labeling recommendations to guide their identification and use.},
}

@article {pmid40119445,
year = {2025},
author = {Niaz, H and Skurnik, M and Adnan, F},
title = {Genomic and proteomic characterization of four novel Schitoviridae family phages targeting uropathogenic Escherichia coli strain.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {83},
pmid = {40119445},
issn = {1743-422X},
mesh = {Humans ; *Genome, Viral ; *Uropathogenic Escherichia coli/virology/genetics ; *Host Specificity ; *Phylogeny ; *Proteomics ; Genomics ; Phage Therapy ; Urinary Tract Infections/microbiology/virology ; Escherichia coli Infections/microbiology ; Coliphages/genetics/isolation & purification/ultrastructure/classification/physiology ; Wastewater/virology/microbiology ; Proteome ; Bacteriophages/genetics/isolation & purification/classification/ultrastructure/physiology ; },
abstract = {BACKGROUND: Escherichia coli-associated urinary tract infections (UTIs) are among the most prevalent bacterial infections in humans. Typically, antibiotic medication is used to treat UTIs, but over the time, growth of multidrug resistance among these bacteria has created a global public health issue that necessitates other treatment modalities, such as phage therapy.

METHODS: The UPEC strain PSU-5266 (UE-17) was isolated from human urine samples, while phages were obtained from wastewater. These phages were characterized through host range analysis, stability studies, adsorption assays, and electron microscopy. Additionally, genomic, phylogenetic, and proteomic analyses were conducted to provide further insights.

RESULTS: The current study describes the isolation and characterization of four Escherichia coli phages designated as UE-S5a, UE-S5b, UE-M3 and UE-M6. Bactericidal assays depicted that all bacteriophages exhibited a strong lytic ability against uropathogenic E. coli (UPEC) strain PSU-5266 (UE-17). The phages displayed a broad host range (31-41%) among 104 tested isolates and adsorption rate of 15-20 min. They were stable within pH range of 5-11 and temperature range of 4 to 55 °C. Electron microscopy showed that all phages have icosahedral heads (70-74 nm) and short non-contractile tails, thus exhibiting a podovirus morphology. Sequencing results showed that they have linear double stranded DNA, genome of 73 to 76 kb in length, with GC content of 42% and short direct terminal repeats. Their genomes contain 84-88 predicted genes with putative functions predicted to 42-48% of gene products. The phylogenetic and comparative genomic analysis results depicted that these phages, sharing > 98% sequence similarity, are new members of genus Gamaleyavirus of subfamily Enquatrovirinae, in the Schitoviridae family. Mass spectrometric analysis of purified phage particles identified 44-56 phage particle-associated proteins (PPAPs) belonging to various functional groups such as lysis proteins, structural proteins, DNA packaging related proteins, and proteins involved in replication, metabolism and regulation. In addition, no genes encoding virulence factors, antibiotic resistance or lysogeny factors were identified.

CONCLUSION: The overall findings suggest that these bacteriophages are potential candidates for phage therapy in treating UTIs caused by UPEC strains.},
}

Humans
*Genome, Viral
*Uropathogenic Escherichia coli/virology/genetics
*Host Specificity
*Phylogeny
*Proteomics
Genomics
Phage Therapy
Urinary Tract Infections/microbiology/virology
Escherichia coli Infections/microbiology
Coliphages/genetics/isolation & purification/ultrastructure/classification/physiology
Wastewater/virology/microbiology
Proteome
Bacteriophages/genetics/isolation & purification/classification/ultrastructure/physiology

@article {pmid40119155,
year = {2025},
author = {Heidrich, V and Valles-Colomer, M and Segata, N},
title = {Human microbiome acquisition and transmission.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40119155},
issn = {1740-1534},
abstract = {As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.},
}

@article {pmid40116497,
year = {2025},
author = {Moreland, RB and Choi, BI and Fontes Noronha, M and Baker, J and Kaindl, J and Wolfe, AJ},
title = {Complete genome sequence of Trueperella bernardiae strain UMB8254, isolated from the bladder of a female with metabolic syndrome and nephrolithiasis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126524},
doi = {10.1128/mra.01265-24},
pmid = {40116497},
issn = {2576-098X},
abstract = {Trueperella bernardiae is infrequently isolated, usually in polymicrobial communities, from human hosts with a wide variety of symptoms and diseases. Here, we report a complete genome sequence of Trueperella bernardiae (UMB8254), isolated from the bladder of a human female with metabolic syndrome and nephrolithiasis.},
}

@article {pmid40111698,
year = {2025},
author = {Vernon, JJ},
title = {Modulation of the Human Microbiome: Probiotics, Prebiotics, and Microbial Transplants.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {277-294},
pmid = {40111698},
issn = {0065-2598},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Probiotics/therapeutic use ; *Microbiota/physiology ; Mouth/microbiology ; Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; },
abstract = {The balance between health and disease is intrinsically linked to the interactions between microbial communities and the host. This complex environment of antagonism and synergy involves both prokaryotic and eukaryotic cells, whose collaborative metabolic pathways and immunomodulatory elements influence system homeostasis. As with the gut and other niches, the oral microbiome has the capacity to affect distal host sites. The ability to manipulate this environment holds the potential to impact local and systemic disease.With the increasing threat of antimicrobial resistance, novel approaches to reduce the burden of disease are essential. The use of probiotics and prebiotics is one such strategy. Probiotics introduce non-pathogenic bacteria into the environment to compete with pathogens for nutrients and attachment sites, or to produce metabolites that counteract disease aetiologies. Prebiotic compounds enhance the growth of health-associated organisms, offering additional benefits, whilst a conjunctive approach with probiotics potentially holds even greater promise. Though widely studied in the gastrointestinal context, their potential for treating oral diseases, such as dental caries and periodontitis, is less understood. Additionally, the use of microbial transplantations has demonstrated efficacy in other areas, reducing systemic inflammation and recolonising with commensal bacteria. Here we evaluate their use in the oral context and their modulatory impact on overall health.In this chapter, we discuss how pro- and prebiotic strategies seek to modulate both the oral and gut environments to promote oral health and prevent disease. We assess novel approaches for utilising health-associated microorganisms to combat oral disorders, either administered locally in the mouth or imparting influence through immune modulation via the oral-gut axis. By examining available clinical trial data, we aim to further understand the intricacies involved in this discipline. Furthermore, we consider the challenges facing the research community, including optimal candidate organism/compound selection and colonisation retention, as well as considerations for future research.},
}

Humans
*Prebiotics/administration & dosage
*Probiotics/therapeutic use
*Microbiota/physiology
Mouth/microbiology
Gastrointestinal Microbiome/physiology
Fecal Microbiota Transplantation/methods

@article {pmid40111686,
year = {2025},
author = {Colombo, APV and Lourenço, TGB and de Oliveira, AM and da Costa, ALA},
title = {Link Between Oral and Gut Microbiomes: The Oral-Gut Axis.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {71-87},
pmid = {40111686},
issn = {0065-2598},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Dysbiosis/microbiology ; Animals ; Gastrointestinal Tract/microbiology ; },
abstract = {In the last decades, groundbreaking research on the human microbiome has changed our reductionist conception of the etiology and pathogenesis of several chronic diseases. As a result, we have come to appreciate the significance of a balanced microbiome in maintaining human health. In this context, the upper and lower gastrointestinal tracts (GITs) comprise the most abundant and diverse microbiotas of the human body. In addition to its diversity, functional redundancy, and temporal stability, a healthy GIT microbiome is characterized by its body site specificity. In fact, current evidence has indicated that the translocation of oral species to the gut environment through the oral-gut axis is increased in an array of illnesses, including chronic inflammatory and metabolic diseases, neurological disorders, and cancer. Oral pathogens have also been shown to promote gut dysbiosis and systemic inflammation in animal models. Yet, some level of overlapping between oral and gut microbiomes may occur without disruption of these microbial communities and loss of site specificity. The uniqueness of each host-microbiome entity may hinder our ability to define a "universal" normal GIT microbiome. Despite that, this chapter summarizes the predominant health-related taxa along the human GIT, as well as their role in the physiology and immunity of the digestive system. Some mechanisms that may lead to disturbances and relevant shifts in the oral and gut microbiomes of major inflammatory chronic diseases are also pointed out. Lastly, oral-fecal microbial signatures are presented as potential biomarkers for several oral and systemic disorders. The recognition of such symbiotic/dysbiotic microbial profiles may provide insights into the development of more accurate early diagnosis and therapeutic ecological approaches to restore the balance of the GIT microbiome.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mouth/microbiology
*Dysbiosis/microbiology
Animals
Gastrointestinal Tract/microbiology

@article {pmid40111682,
year = {2025},
author = {Dame-Teixeira, N and Do, T and Deng, D},
title = {The Oral Microbiome and Us.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {3-9},
pmid = {40111682},
issn = {0065-2598},
mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; *Dysbiosis/microbiology ; Periodontitis/microbiology ; Animals ; Oral Health ; },
abstract = {Oral and systemic human health depend on the symbiotic relationship between the human host and its microbiome. As the second most diverse site of the human microbiome, the oral cavity is instrumental in symbiotic relationships, transforming nutrients and acting as the human body's initial barrier against pathogens. However, under certain conditions, the typically beneficial oral microbiome can become harmful. Systemic inflammatory diseases can send signals through the oral-gut axis, such as cytokines and host defensins, altering gene expression and, consequently, the composition of the oral microbiome. These changes can be responsible for causing oral diseases, such as periodontitis and candidiasis. Evidence of metabolic syndrome, including obesity, hypertension, hyperglycemia, and dyslipidemia, exacerbates oral microbiome dysbiosis. On the other hand, the oral microbiota can also influence systemic health. Inflammatory processes in the gingival structures caused by a dysbiotic oral microbiome are linked to worsen glycemic levels in diabetics, premature birth, and rheumatoid arthritis, among others. The idea for this book emerged from the need to explore the multifaceted nature of this relationship in its various dimensions. We discuss multispecies characteristics from an ecological perspective, focusing on how the host affects the microbiome and vice versa. Understanding how the oral microbiome influences human health will guide tailored strategies for disease prevention and treatment, which is discussed in the last section of the book. Looking ahead, predictive health and disease models will enable personalized therapies centered on restoring the healthy human microbiome.},
}

Humans
*Mouth/microbiology
*Microbiota/physiology
*Dysbiosis/microbiology
Periodontitis/microbiology
Animals
Oral Health

@article {pmid40111647,
year = {2025},
author = {Choi, Y and Jeong, J and Kim, M and Cha, S and Han, K},
title = {Backtracking identification techniques for predicting unclear bacterial taxonomy at species level: molecular diagnosis-based bacterial classification.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {40111647},
issn = {2092-9293},
support = {RS-2024-00355393//National Institute for International Education/ ; },
abstract = {Bacterial 16S rRNA genes are widely used to classify bacterial communities within interesting environments (e.g., plants, water, human body) because they contain nine hyper-variable regions (V1-V9) reflecting a large number of sequence variation sites between species. Short-read sequencing platform (targeting partial region of 16S rRNA gene; approximately 150-500 bp) commonly used in the 16S-based microbiome study is favored by many researchers because it is economical and can generate highthroughput sequencing data faster than long-read sequencing platforms. However, this sequencing platform has technical limitations in that it cannot clarify bacterial classification at the species level compared to long-read sequencing technology, which can cover the unclassification issue due to sequence similarity between species by targeting the 16S full-length region. In recent microbiome research-related industries, species-level high-resolution microbial classification is considered a key challenge to secure microbial resources among institutions in the field. However, the long-read sequencing platforms currently offered are still under price adjustment (demanding higher cost than short-read sequencing platforms) and have the disadvantage of low base-calling accuracy compared to short-read sequencing platforms. Therefore, this brief communication introduces the'Molecular diagnosis-based bacterial classification' technology to predict candidate species by backtracking for unclassified bacterial taxonomy at the species level in the NGS-based 16S microbiome study.},
}

@article {pmid40110560,
year = {2025},
author = {Adachi, A and Zhang, F and Kanaya, S and Ono, N},
title = {Quantifying uncertainty in microbiome-based prediction using Gaussian processes with microbial community dissimilarities.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf045},
pmid = {40110560},
issn = {2635-0041},
abstract = {SUMMARY: The human microbiome is closely associated with the health and disease of the human host. Machine learning models have recently utilized the human microbiome to predict health conditions and disease status. Quantifying predictive uncertainty is essential for the reliable application of these microbiome-based prediction models in clinical settings. However, uncertainty quantification in such prediction models remains unexplored. In this study, we have developed a probabilistic prediction model using a Gaussian process (GP) with a kernel function that incorporates microbial community dissimilarities. We evaluated the performance of probabilistic prediction across three regression tasks: chronological age, body mass index, and disease severity, using publicly available human gut microbiome datasets. The results demonstrated that our model outperformed existing methods in terms of probabilistic prediction accuracy. Furthermore, we found that the confidence levels closely matched the empirical coverage and that data points predicted with lower uncertainty corresponded to lower prediction errors. These findings suggest that GP regression models incorporating community dissimilarities effectively capture the characteristics of phylogenetic, high-dimensional, and sparse microbial abundance data. Our study provides a more reliable framework for microbiome-based prediction, potentially advancing the application of microbiome data in health monitoring and disease diagnosis in clinical settings.

The code is available at https://github.com/asahiadachi/gp4microbiome.},
}

@article {pmid39854218,
year = {2025},
author = {Zeng, T and Sun, K and Mai, L and Hong, X and He, X and Lin, W and Chen, S and Yan, L},
title = {Extracellular Vesicle-Associated miR-ERIA Exerts the Antiangiogenic Effect of Macrophages in Diabetic Wound Healing.},
journal = {Diabetes},
volume = {74},
number = {4},
pages = {596-610},
doi = {10.2337/db24-0701},
pmid = {39854218},
issn = {1939-327X},
support = {82222014//The National Natural Science Foundation of China Excellent Young Scientists Fund/ ; 2023A03J0706//Ministry of Education, China; Guangzhou Science and Technology Program/ ; 2020B1111170009//Guangdong Clinical Research Center for Metabolic Diseases/ ; 202102100004//Guangzhou Key Laboratory for Metabolic Diseases/ ; 32271185//The National Natural Science Foundation of China/ ; Sun Yat-sen University//Key Laboratory of Human Microbiome and Chronic Diseases/ ; 82200902//National Natural Science Foundation of China/ ; },
mesh = {*Wound Healing/drug effects/physiology ; *Extracellular Vesicles/metabolism ; *MicroRNAs/metabolism/genetics ; *Macrophages/metabolism/drug effects ; Animals ; Humans ; Mice ; Glycation End Products, Advanced/metabolism ; Cell Movement/drug effects ; Human Umbilical Vein Endothelial Cells/metabolism ; Endothelial Cells/metabolism/drug effects ; Angiogenesis Inhibitors/pharmacology/therapeutic use ; Skin Ulcer/metabolism/genetics ; Diabetes Mellitus, Experimental/metabolism ; },
abstract = {An understanding of cell interactions is needed to identify therapeutic targets for diabetic cutaneous ulcers. We explored extracellular vesicles after treatment with advanced glycation end products (AGEs-EVs) derived from macrophages that can suppress diabetic cutaneous wound healing. We found that a novel miRNA enriched in AGEs-EVs (miR-ERIA) suppresses the migration and tube formation of vascular endothelial cells by targeting helicase with zinc finger 2. miR-ERIA offers a potential therapeutic target for diabetic cutaneous ulcers.},
}

*Wound Healing/drug effects/physiology
*Extracellular Vesicles/metabolism
*MicroRNAs/metabolism/genetics
*Macrophages/metabolism/drug effects
Animals
Humans
Mice
Glycation End Products, Advanced/metabolism
Cell Movement/drug effects
Human Umbilical Vein Endothelial Cells/metabolism
Endothelial Cells/metabolism/drug effects
Angiogenesis Inhibitors/pharmacology/therapeutic use
Skin Ulcer/metabolism/genetics
Diabetes Mellitus, Experimental/metabolism

@article {pmid40102379,
year = {2025},
author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T},
title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2683},
pmid = {40102379},
issn = {2041-1723},
support = {OPP1175213//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; },
abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
*Dietary Supplements
Infant
Pregnancy
Adult
Burkina Faso
*Carbohydrate Metabolism
Infant, Newborn
Feces/microbiology
Dietary Proteins/metabolism
Male
Lactation

@article {pmid40099907,
year = {2025},
author = {Reetz, L and Schulze, L and Kronenberger, T and Selim, KA and Schaefle, T and Dema, T and Zipperer, A and Mößner, J and Poso, A and Grond, S and Peschel, A and Krismer, B},
title = {The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism.},
journal = {mBio},
volume = {},
number = {},
pages = {e0357124},
doi = {10.1128/mbio.03571-24},
pmid = {40099907},
issn = {2150-7511},
abstract = {Many human microbiome members inhibit bacterial competitors by production of antimicrobial compounds whose expression needs to be tightly controlled to balance the costs and benefits of compound biosynthesis. The nasal commensal Staphylococcus lugdunensis outcompetes Staphylococcus aureus using the antimicrobial lugdunin. The lugdunin biosynthetic gene cluster (BGC) encodes two potential regulators whose roles have remained unknown. Deletion of the regulator genes lugR or lugJ led to increased lugdunin production and/or immunity. While LugR was found to repress the transcription of the biosynthetic lugRABCTDZ operon, LugJ repressed the lugIEFGH export and immunity genes. Both regulators bound to different inverted repeats in the controlled promoter regions. Notably, both repressors were released from cognate promoters to allow transcription upon addition of exogenous lugdunin. Even minor structural changes disabled lugdunin derivatives to induce expression of its BGC, which is consistent with inferior binding to the predicted LugR and LugJ binding pockets. Thus, lugdunin controls its own biosynthesis through a feed-forward mechanism probably to avoid futile production.IMPORTANCEBiosynthetic gene clusters (BGCs) are usually tightly controlled to avoid production of costly goods at inappropriate time points or unfavorable conditions. However, in most cases, the regulatory signals of these clusters have remained unknown. Frequently, quorum sensing or two-component regulatory systems are involved in BGC expression control. This study elucidates the sophisticated regulation of lugdunin biosynthesis and secretion via two independent regulators, LugR and LugJ. Although belonging to different families of repressors, both directly interact with the antimicrobial lugdunin and thereby enhance biosynthesis and secretion in a feed forward-like mechanism.},
}

@article {pmid40086654,
year = {2025},
author = {Pietilä, JP and Häkkinen, T and Ollgren, J and Kantele, A},
title = {Modelling international travel as risk of acquiring Dientamoeba fragilis: comparison to Giardia duodenalis data.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102836},
doi = {10.1016/j.tmaid.2025.102836},
pmid = {40086654},
issn = {1873-0442},
abstract = {BACKGROUND: The intestinal parasite Dientamoeba fragilis (DF) is spread worldwide and can cause prolonged gastrointestinal symptoms, yet its link to international travel has been scarcely studied. To explore this connection, we examined the association between DF cases and international travel history by destination, comparing the findings to data on Giardia duodenalis (GD), a common travel-acquired intestinal parasite.

METHODS: We analysed clinical data from patients with DF or GD infection in the Helsinki Metropolitan Area, categorizing the patients as travellers and non-travellers on the basis of their travel history. To assess acquisition risk by destination, we devised a DF/GD risk score (RS) relating case numbers to travel volumes as denominators in each destination, with travel data retrieved from the Official Statistics of Finland (OSF).

RESULTS: Travel history was reported less frequently by patients with DF (30%) than GD (60%). DF had the highest RSs for Africa (41.3), followed by Asia and Oceania (17.9) and the Americas (11.5). The respective GD RSs were 32.8, 25.4, and 11.9. The lowest RSs for both parasites were recorded for Eastern and Western Europe, Russia and the Baltic countries, and Scandinavia. For Asia and Oceania, the GD RS exceeded that of DF; for the other sites, DF had higher RSs than GD.

CONCLUSIONS: Dientamoeba fragilis appears to be transmitted both domestically and internationally. Although the overall acquisition risk appears low, for both Dientamoeba fragilis and Giardia duodenalis, the highest RSs are linked to visits to (sub)tropical regions, with subregional differences between the two parasites.},
}

@article {pmid40084887,
year = {2025},
author = {Sun, Y-Y and Liu, N-N},
title = {Mycobiome: an underexplored kingdom in cancer.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0026124},
doi = {10.1128/mmbr.00261-24},
pmid = {40084887},
issn = {1098-5557},
abstract = {SUMMARYThe human microbiome, including bacteria, fungi, archaea, and viruses, is intimately linked to both health and disease. The relationship between bacteria and disease has received much attention and intensive investigation, while that of the fungal microbiome, also known as mycobiome, has lagged far behind bacteria. There is growing evidence showing mycobiome dysbiosis in cancer patients, and certain cancer-specific fungi may contribute to cancer progression by interacting with both host and bacteria. It was also demonstrated that the role of fungi-derived products in cancer should also not be underestimated. Therefore, investigating how fungal pathogenesis contributes to the onset and spread of cancer would yield crucial information for cancer diagnosis, prevention, and anti-cancer therapy.},
}

@article {pmid40084234,
year = {2019},
author = {Werlang, C and Cárcarmo-Oyarce, G and Ribbeck, K},
title = {Engineering mucus to study and influence the microbiome.},
journal = {Nature reviews. Materials},
volume = {4},
number = {2},
pages = {134-145},
pmid = {40084234},
issn = {2058-8437},
abstract = {Mucus is a 3D hydrogel that houses the majority of the human microbiome. The mucous environment plays an important role in the differentiation and behaviour of microbial phenotypes and enables the creation of spatial distributions. Dysregulation of mucus is further associated with various diseases. Therefore, mucus is the key ingredient to study the behaviour of commensal and pathogenic microbiota in vitro. Indeed, microorganisms cultured in mucus exhibit phenotypes substantially different from those exhibited in standard laboratory media. In this Review, we discuss the impact of mucus on the microbiome and examine the structure and glycosylation of mucins - the main building blocks of mucus. We investigate the impact of glycans on mucin function and highlight different approaches for the engineering of synthetic mucins, including synthesis of the backbone, the design of mucin-mimetic hydrogels and the engineering of glycans. Finally, mucin mimetics for 3D in vitro cell culture and for modulating microbial community structure and function are discussed.},
}

@article {pmid40077792,
year = {2025},
author = {Costa, CJ and Prescott, S and Fourie, NH and Abey, SK and Sherwin, LB and Rahim-Williams, B and Joseph, PV and Posada-Quintero, H and Hoffman, RK and Henderson, WA},
title = {Host Transcriptome and Microbial Variation in Relation to Visceral Hyperalgesia.},
journal = {Nutrients},
volume = {17},
number = {5},
pages = {},
doi = {10.3390/nu17050921},
pmid = {40077792},
issn = {2072-6643},
support = {1ZIANR000018-01-09; K22MD006143-01/GF/NIH HHS/United States ; },
mesh = {Humans ; *Hyperalgesia/microbiology ; *Transcriptome ; Male ; Female ; Adult ; Visceral Pain/microbiology ; Microbiota ; RNA, Messenger/metabolism ; Middle Aged ; Mouth/microbiology ; Gastrointestinal Microbiome ; Bacteria/genetics/classification ; Young Adult ; },
abstract = {BACKGROUND: Chronic visceral hypersensitivity is associated with an overstressed pain response to noxious stimuli (hyperalgesia). Microbiota are active modulators of host biology and are implicated in the etiology of visceral hypersensitivity.

OBJECTIVES: we studied the association between the circulating mRNA transcriptome, the intensity of induced visceral pain (IVP), and variation in the oral microbiome among participants with and without baseline visceral hypersensitivity.

METHODS: Transcriptomic profiles and microbial abundance were correlated with IVP intensity. Host mRNA and microbes associated with IVP were explored, linking variation in the microbiome to host RNA biology.

RESULTS: 259 OTUs were found to be associated with IVP through correlation to differential expression of 471 genes in molecular pathways related to inflammation and neural mechanisms, including Rho and PI3K/AKT pathways. The bacterial families Lachnospiraceae, Prevotellaceae, and Veillonellaceae showed the highest degree of association. Oral microbial profiles with reduced diversity were characteristic of participants with visceral hypersensitivity.

CONCLUSIONS: Our results suggest that the oral microbiome may be involved in systemic immune and inflammatory effects and play a role in nervous system and stem cell pathways. The interactions between visceral hypersensitivity, differentially expressed molecular pathways, and microbiota described here provide a framework for further work exploring the relationship between host and microbiome.},
}

Humans
*Hyperalgesia/microbiology
*Transcriptome
Male
Female
Adult
Visceral Pain/microbiology
Microbiota
RNA, Messenger/metabolism
Middle Aged
Mouth/microbiology
Gastrointestinal Microbiome
Bacteria/genetics/classification
Young Adult

@article {pmid40076446,
year = {2025},
author = {Li, Y and Zhang, ZJ and Saarela, O and Sharma, D and Xu, W},
title = {Mediation CNN (Med-CNN) Model for High-Dimensional Mediation Data.},
journal = {International journal of molecular sciences},
volume = {26},
number = {5},
pages = {},
doi = {10.3390/ijms26051819},
pmid = {40076446},
issn = {1422-0067},
support = {RGPIN-2024-06081//Natural Sciences and Engineering Research Council/ ; },
mesh = {Humans ; *Algorithms ; *Neural Networks, Computer ; *Microbiota ; Female ; Computer Simulation ; },
abstract = {Complex biological features such as the human microbiome and gene expressions play a crucial role in human health by mediating various biomedical processes that influence disease progression, such as immune responses and metabolic processes. Understanding these mediation roles is essential for gaining insights into disease pathogenesis and improving treatment outcomes. However, analyzing such high-dimensional mediation features presents challenges due to their inherent structural and correlations, such as the hierarchical taxonomic structures in microbial operational taxonomic units (OTUs), gene-pathway relationships, and the high dimensionality of the datasets, which complicates mediation analysis. We propose the Med-CNN model, an iterative approach using Convolutional Neural Networks (CNNs) to incorporate the complex biological network of the mediation features. The output values from network-specific CNN models are condensed into an integrative mediation metric (IMM), which captures essential biological information for estimating mediation effects. Our approach is designed to handle high-dimensional data and accommodate their unique structures and non-linear interactive mediation effects. Through comprehensive simulation studies, we evaluated the performance of our algorithm across different scenarios, including various mediation effects, effect sizes, and sample sizes, and we compared it to conventional methods. Our simulations demonstrated consistently lower biases in mediation effect estimates, with values ranging from 0.17 to 0.56, which were lower than other established methods ranging from 0.24 to 13.27. In a real data application, our method identified a mediation effect of 0.06 between ethnicity and vaginal pH levels.},
}

Humans
*Algorithms
*Neural Networks, Computer
*Microbiota
Female
Computer Simulation

@article {pmid40072660,
year = {2025},
author = {Hu, J and Chen, W and Zhu, R and Yang, F and Xu, J and Xiang, B and Li, Y and Wang, W and Zhu, L and Chen, G and Zhi, M},
title = {Dietary risk factors in Crohn's disease and ulcerative colitis: a cohort study with paired healthy relatives as controls.},
journal = {European journal of nutrition},
volume = {64},
number = {3},
pages = {123},
pmid = {40072660},
issn = {1436-6215},
support = {2014008//Sun Yat-sen University Clinical Research 5010 Program/ ; 82170542//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; 82270544//National Natural Science Foundation of China/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; 2021YFF0703702//National Key Research and Development Program of China/ ; 2023YFF1104404//National Key Research and Development Program of China/ ; 2023AFD124//Hubei Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Crohn Disease/epidemiology ; *Colitis, Ulcerative/epidemiology ; Female ; Male ; Risk Factors ; Adult ; *Diet/methods/statistics & numerical data ; Cohort Studies ; Middle Aged ; Case-Control Studies ; Family ; Feeding Behavior ; },
abstract = {PURPOSE: Conflicting results have been reported on dietary factors in inflammatory bowel diseases (IBDs). Here, we compared the dietary intakes of IBD patients with those of paired healthy relatives (HRs), aiming to minimize the impact of genetic and environmental confounders.

METHODS: Patients with Crohn's disease (CD, N = 45) and ulcerative colitis (UC, N = 20), their paired HRs (NCD-HR = 45, NUC-HR = 20) and healthy non-relative (HNR, NCD-HNR = 25, NUC-HNR = 55) controls were recruited. Participants have kept dietary habits since the onset of IBDs and report no other recent digestive diseases or surgeries. Pre-illness dietary factors were assessed through 24-hour recall interviews. Statistical analyses included Analysis of Variance, Fisher's exact tests, Wilcoxon rank sum tests, logistic regressions, Area Under the Receiver-Operator Curve (AUROC) analysis, and Least Absolute Shrinkage and Selection Operator (LASSO) regression.

RESULTS: Dietary features identified in IBD patients using the HR controls differed from those identified using the HNR controls. For CD, lower intakes of vitamin C, dietary fiber, calcium, vegetables, decanoic acid (10:0), milk, dairy foods, and β-carotene were identified as risk factors when compared to HRs. LASSO regression highlighted milk, vegetables, and vitamin C as the most significant risk factors for CD. In UC patients, lower intakes of phosphorus, docosapentaenoic acid (DPA, 22:5, n-3), vitamins B-2 and B-12, and choline, along with a higher intake of α-carotene, were identified as risk factors compared to HRs. LASSO regression emphasized DPA, vitamins B-2 and B-12, and α-carotene as the most significant risk factors for UC.

CONCLUSION: Monitoring dietary intake patterns is crucial for the prevention and personalized treatment of CD and UC.},
}

Humans
*Crohn Disease/epidemiology
*Colitis, Ulcerative/epidemiology
Female
Male
Risk Factors
Adult
*Diet/methods/statistics & numerical data
Cohort Studies
Middle Aged
Case-Control Studies
Family
Feeding Behavior