@article {pmid40229501,
year = {2025},
author = {Chattrakulchai, K and Pongchaikul, P and Wattanayingcharoenchai, R and Tantitham, C and Manonai, J},
title = {Urinary microbiomes in postmenopausal women with or without urinary symptoms of the genitourinary syndrome of menopause: a cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12796},
pmid = {40229501},
issn = {2045-2322},
support = {RF_65055//Faculty of Medicine Ramathibodi Hospital This study is supported by Faculty of Medicine Ramathibodi Hospital/ ; },
mesh = {Humans ; Female ; *Microbiota ; *Postmenopause/urine ; Middle Aged ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Female Urogenital Diseases/microbiology/urine ; Syndrome ; Aged ; *Menopause ; },
abstract = {Some postmenopausal women suffer from genital and urinary symptoms, while others do not. Therefore, the hypoestrogenic status cannot entirely explain the occurrence of the genitourinary syndrome in menopause (GSM). Differences in the urinary microbiome might play a role in bladder function and vulnerability to urinary symptoms. This study aimed to compare characterization urinary microbiome in postmenopausal women who experienced GSM with urinary symptoms with that in those without urinary symptoms. Forty participants were screened for genital symptoms of GSM and then divided into the urinary symptoms group and the non-urinary symptoms group on the basis of a validated questionnaire. 16 S rRNA gene sequencing was performed to investigate microbial diversity. The alpha diversity was used to evaluate the species richness and evenness, while the beta diversity was used to estimate the differences in the urinary microbiome between the groups. Differential abundance analysis was used to investigate biomarkers in the groups by linear discriminant analysis effect size. The relationship between the urinary microbiome and urinary symptoms was assessed using Spearman's correlation analysis. The characteristics of the participants were not different between the groups. Gardnerella was found in 22.2% (4/18) and 11.1% (2/18) of participants in the urinary symptoms group and in the non-urinary symptoms group, respectively (p > 0.05). Alpha diversity was less in the urinary symptoms group than in the non-urinary symptoms group, but this was not significant. Beta diversity of the urinary microbiome was not significantly different between the two groups. A differential abundance analysis showed that the genus Prevotella was significantly dominant in postmenopausal women with GSM who reported urinary symptoms. Prevotella was marginally correlated with voiding symptoms (r[2] = 0.44; p = 0.01). The bladder or urinary microbiome is closely related to urinary symptoms of GSM. Species richness and diversity are not significantly different between postmenopausal women with GSM with and without urinary symptoms. Prevotella is dominant in symptomatic women and slightly correlated with voiding symptoms.},
}

Humans
Female
*Microbiota
*Postmenopause/urine
Middle Aged
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
*Female Urogenital Diseases/microbiology/urine
Syndrome
Aged
*Menopause

@article {pmid40229352,
year = {2025},
author = {Valido, E and Bertolo, A and Wöllner, J and Pannek, J and Krebs, J and Stoyanov, J},
title = {Effects of Uro-Vaxom vs. placebo on the urinary tract microbiome in individuals with spinal cord injury in a randomized controlled pilot trial (Uro-Vaxom pilot).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {12825},
pmid = {40229352},
issn = {2045-2322},
support = {801076//European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement/ ; },
mesh = {Humans ; *Spinal Cord Injuries/microbiology/complications/drug therapy ; Pilot Projects ; Male ; Female ; Middle Aged ; *Microbiota/drug effects ; Adult ; *Urinary Tract Infections/microbiology/drug therapy ; *Urinary Tract/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; Escherichia coli/isolation & purification ; },
abstract = {Individuals with spinal cord injury/disease (SCI/D) have a high incidence of urinary tract infections (UTI). This randomized controlled pilot trial investigated the effect of an immunomodulator (Uro-Vaxom) versus a placebo on the urinary tract microbiome of individuals with SCI/D to inform the design of a larger trial. Twenty participants with SCI/D undergoing primary rehabilitation were randomized to receive either Uro-Vaxom or a placebo for three months (ClinicalTrials.gov NCT04049994 08/08/2019). Urine was collected at baseline, immediately post-treatment, and three months post-treatment. DNA was extracted and sequenced using full-length 16 S rRNA using Oxford Nanopore technology. Internal controls were added for absolute abundance estimation. There were 10 participants in Uro-Vaxom and 10 in placebo analyzed. The prevalence of Escherichia coli was lower in the Uro-Vaxom group (2/10) compared to the placebo group (5/10) post-treatment, although this difference was not statistically significant. Significant alpha and beta diversity differences were associated with the microbial load, sex, and voiding method. Uro-Vaxom showed potential in reducing E. coli prevalence during the treatment period, but this result requires validation in a larger trial. Future trials should consider the baseline microbial load and optimal timing of intervention to ensure that the observed effects are attributable to immunomodulation.},
}

Humans
*Spinal Cord Injuries/microbiology/complications/drug therapy
Pilot Projects
Male
Female
Middle Aged
*Microbiota/drug effects
Adult
*Urinary Tract Infections/microbiology/drug therapy
*Urinary Tract/microbiology/drug effects
RNA, Ribosomal, 16S/genetics
Escherichia coli/isolation & purification

@article {pmid40228808,
year = {2025},
author = {Jones, KR and Duong, T and Sacci, O and Gregory, CL and Belden, LK},
title = {Amphibian bacterial communities assemble variably among host species, across development, and between similar habitats.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf014},
pmid = {40228808},
issn = {1557-7023},
abstract = {Symbiotic host-associated microbial communities are nearly ubiquitous and are often essential to host growth and development. The assembly of these communities on hosts is the result of a combination of the processes of selection, dispersal, and drift. For some species, essential symbionts are quickly acquired from the environment during embryonic development, while others may vertically acquire symbionts from parents. For amphibians with complex life cycles that undergo metamorphosis, an additional physiological transition from larval to adult forms may represent another distinct developmental window for bacterial colonization. Prior research has demonstrated that metamorphosis impacts the composition of amphibian-associated bacterial communities, however, we do not know whether similar shifts occur during metamorphosis across different amphibian species. To more clearly understand patterns in microbiome development across host species within a given area, we assessed the bacterial communities associated with eggs from five locally-occurring amphibian species and tadpoles and juveniles from four of the species. Additionally, to determine if stochasticity result in varied microbiome composition among conspecifics, we raised one species, spring peepers (Pseudacris crucifer), in outdoor 1000 L mesocosms. Through 16S rRNA gene amplicon sequencing, we detected distinct bacterial communities across amphibian species and development. Additionally, we found that tadpoles harbored different communities of bacteria in the different mesocosms, suggesting that stochasticity may play a large role in bacterial assembly on tadpoles. Our results serve to deepen our understanding of natural shifts in amphibian-associated bacterial communities and how these shifts are host-species dependent. Additionally, this study provides support for the idea that stochasticity in the form of drift or priority effects can drive individual variation in microbiome composition among hosts.},
}

@article {pmid40228747,
year = {2025},
author = {Wang, Z and Wang, X and Liu, Z and Huang, F and Pan, Z and Zhang, Z and Liu, T},
title = {Nutritional strategies in oncology: The role of dietary patterns in modulating tumor progression and treatment response.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189322},
doi = {10.1016/j.bbcan.2025.189322},
pmid = {40228747},
issn = {1879-2561},
abstract = {Dietary interventions can influence tumor growth by restricting tumor-specific nutritional requirements, altering the nutrient availability in the tumor microenvironment, or enhancing the cytotoxicity of anticancer drugs. Metabolic reprogramming of tumor cells, as a significant hallmark of tumor progression, has a profound impact on immune regulation, severely hindering tumor eradication. Dietary interventions can modify tumor metabolic processes to some extent, thereby further improving the efficacy of tumor treatment. In this review, we emphasize the impact of dietary patterns on tumor progression. By exploring the metabolic differences of nutrients in normal cells versus cancer cells, we further clarify how dietary patterns influence cancer treatment. We also discuss the effects of dietary patterns on traditional treatments such as immunotherapy, chemotherapy, radiotherapy, and the gut microbiome, thereby underscoring the importance of precision nutrition.},
}

@article {pmid40228704,
year = {2025},
author = {Ahmed, F and Abu-El-Haija, M},
title = {Acute Pancreatitis in Children: It's Not Just a Simple Attack.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.04.001},
pmid = {40228704},
issn = {1528-0012},
abstract = {Acute pancreatitis (AP) in children presents unique challenges distinct from adult manifestations, requiring specialized diagnostic and therapeutic approaches. Compared to adults, pediatric AP has lower mortality rates but still carries significant morbidity and potential long-term complications. This review examines current evidence on pediatric AP, highlighting recent advances in diagnosis, risk stratification, and management strategies. Current diagnostic approaches utilize serum lipase and amylase testing, along with various imaging modalities that have different diagnostic values. Recent research has identified promising biomarkers for predicting severe acute pancreatitis (SAP), including blood urea nitrogen, C-reactive protein, and specific cytokine signals. Emerging evidence suggests a role of gut microbiome dysbiosis in disease pathogenesis, opening new therapeutic possibilities targeting the gut-pancreas axis. Genetic factors, specifically pancreatitis risk genes, influence disease progression to recurrent and chronic pancreatitis. In this review, we summarize the consequences of an isolated AP episode in children. Our review highlights for the first time how AP can lead to significant long-term sequelae, including exocrine/nutritional deficiencies, endocrine pancreatic dysfunction, diabetes, recurrent pain, and decreased quality of life compared to healthy population controls. The goal of this review is to summarize advances in understanding of pediatric AP and to emphasize the importance of early recognition, appropriate risk stratification, and comprehensive follow-up after the first pediatric AP episode, while highlighting areas requiring future research to optimize patient outcomes.},
}

@article {pmid40228484,
year = {2025},
author = {Arrieta, MC},
title = {Microbiome Maturation Trajectory and Key Milestones in Early Life.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-8},
doi = {10.1159/000543754},
pmid = {40228484},
issn = {1421-9697},
abstract = {BACKGROUND: The development of the gut microbiome during early life plays a critical role in shaping long-term health. The first 1,000 days represent a crucial period in which the microbiome is particularly malleable, influenced by various factors such as birth mode, diet, antibiotic exposure, and environmental interactions.

SUMMARY: This review outlines the key stages of microbiome maturation, beginning with initial colonization at birth and progressing through the diversification and stabilization phases during the first 5 years of life. Factors like breastfeeding, the introduction of solid foods, and early-life antibiotic have a critical impact on microbial diversity and immune system development. Disruptions to the microbiome during this critical window, particularly through antibiotic use, are associated with an increased risk of immune, metabolic, and neurodevelopmental disorders. Recent research emphasizes the need for a better understanding of these early-life trajectories to inform interventions that promote a healthy microbiome.},
}

@article {pmid40228454,
year = {2025},
author = {Asif, A and Koner, S and Hsu, PC and He, BJ and Paul, S and Hussain, B and Hsu, BM},
title = {Synergistic interactions between AMF and MHB communities in the rhizospheric microenvironment facilitated endemic hyperaccumulator plants growth thrive under heavy metal stress in ultramafic soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138233},
doi = {10.1016/j.jhazmat.2025.138233},
pmid = {40228454},
issn = {1873-3336},
abstract = {Ultramafic outcrop settings are characterized by long-term heavy metal (HM) stress and nutrient imbalances, making plant resilience highly challenging. This study investigated that how native plant types in the serpentine environment influence the variation of synergistic interactions between rhizosphere arbuscular mycorrhizal fungi (AMF) and mycorrhizal helper bacteria (MHB) communities under HM stress and nutrient-deficient conditions, which support native plant endemism and their HM accumulation potential. The results displayed significant enrichment of key MHB (Rhizobium_tropici, Bacillus_subtilis, Pseudomonas_parafulva, Pseudomonas_akapagensis) and AMF species (Glomus_constrictum, Glomus_aggregatum, Rhizophagus_intraradices, Rhizophagus_irregularis) in rhizosphere soils (q < 0.05). Pseudomonas_chlororaphis and Burkholderia_cepacia were strongly associated with Rhizophagus_irregularis and Glomus_mosseae in Panicum maximum Jacq (PMJ) and Bidens pilosa (BP) under chromium (Cr), and cadmium (Cd) and arsenic (As) stress. Pseudomonas_fluorescens and Bacillus_pabuli were linked to Geosiphon_pyriformis and Glomus_aggregatum in Pueraria montana (PM) under nickel (Ni), lead (Pb), and cobalt (Co) stress, while Arthrobacter_globiformis and Rhizobium_leguminosarum were associated with Glomus_intraradices under copper (Cu) stress in Leucaena leucocephala (LL). Pathways related to nitrogen, phosphorous and potassium (NPK) cycling, HM detoxification, and resistance were enriched, with AMF predominantly symbiotrophic root-endophytic, except for one as lichenized nostoc endosymbiont. Canonical correspondence analysis (CCA) showed HM stress and nutrients influence MHB-AMF symbiosis, while pH moisture content (MC) and electric conductivity (EC) significantly regulate their distribution. Rhizobium_leguminosarum, Rhizobium_tropici, Nitrospira_japonica, and Rhizobium_cauense with Glomus_mosseae and Rhizophagus_irregularis drive NPK cycling in HM-stressed rhizosphere soils. This finding suggested that association between plants type and their functional rhizosphere microbiome promote an eco-friendly strategy for HM recovery from serpentine soil.},
}

@article {pmid40228374,
year = {2025},
author = {Huo, J and Han, S and Hao, X and Zhou, Z and Lou, J and Li, H and Cao, J and Yu, Y and Mi, W and Liu, Y},
title = {Alterations in the gut microbiome and metabolome in elderly patients with postoperative delirium: A prospective nested case-control study.},
journal = {Journal of clinical anesthesia},
volume = {103},
number = {},
pages = {111833},
doi = {10.1016/j.jclinane.2025.111833},
pmid = {40228374},
issn = {1873-4529},
abstract = {OBJECTIVE: To elucidate the role of gut microbiota and their metabolites, including short-chain fatty acids (SCFAs) and targeted metabolomics, in the development of postoperative delirium (POD) in elderly patients.

DESIGN: Prospective nested case-control study.

SETTING: A Chinese tertiary hospital.

PARTICIPANTS: Elderly patients underwent elective orthopedic surgery.

METHODS: Participants were assessed for POD using the 3-min Diagnostic Confusion Assessment Method (3D-CAM). Biological samples, including feces and plasma, were collected. A 1:1 propensity score matching (PSM) was conducted to match POD cases with non-POD cases. 16S ribosomal RNA (rRNA) sequencing and metabolomics analyses were performed on the matched case series. Predictive models were developed using logistic regression analysis, incorporating bacterial genera and metabolites that exhibited significant differences between the two groups as predictors.

RESULTS: Among 234 patients who were followed up, 41 were diagnosed with POD. A total of 39 cases were matched for both the POD and control groups using PSM. No significant differences were found in the α-diversity and β-diversity of preoperative gut microbiota between the two groups. However, specific bacterial genera, including Romboutsia, Bacteroides faecalis, Blautia mucilaginosa, and Eggerthella lenta, exhibited significant differences. The risk of POD was associated with higher postoperative plasma levels of propionic acid, histidine, aspartate, and ornithine. Logistic regression and receiver operating characteristic curve analyses revealed that indicators derived from the gut microbiota and metabolites could predict POD, with an area under the curve of 0.8413 (95 % confidence interval (CI): 0.7393-0.9434).

CONCLUSION: This study identified four preoperative bacterial genera and four postoperative plasma metabolites associated with an increased risk of POD in elderly orthopedic patients, suggesting the potential of gut microbiota and metabolite profiles as biomarkers for improving risk prediction and guiding interventions.},
}

@article {pmid40228034,
year = {2025},
author = {Shibano, M and Takahashi, M and Nakatsukasa, H and Ishigami, Y and Toyokawa, T and Taira, K and Kawaguchi, T and Nakamura, Y and Kaneda, H},
title = {Proton pump inhibitors reduce nivolumab efficacy in unresectable advanced or recurrent gastric cancer.},
journal = {Immunotherapy},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/1750743X.2025.2491300},
pmid = {40228034},
issn = {1750-7448},
abstract = {BACKGROUND: Proton pump inhibitors (PPI) have been shown to decrease the efficacy of immune checkpoint inhibitors in patients with various cancer types. However, there are few reports on their effect on patients with gastric cancer (GC). Therefore, we investigated the efficacy of nivolumab in patients with GC receiving PPI.

METHODS: This retrospective study analyzed data of patients who received nivolumab monotherapy for unresectable advanced or recurrent GC at Osaka Metropolitan University Hospital between September 2017 and December 2021. The primary and secondary endpoints were progression-free survival (PFS) and overall survival (OS), respectively. PPI use was defined as within 30 days before and after initiation of nivolumab monotherapy.

RESULTS: Seventy-seven eligible patients were included in this analysis. PPIs were used in 33 patients, while 36 patients had a previous gastrectomy. Multivariate analysis revealed that only PPI use was an independent predictor of PFS (hazard ratio [HR] 1.93, 95% confidence interval [CI] 1.03-3.64, p = 0.042). Contrastingly, PPI use was not an independent predictor of OS.

CONCLUSION: PPIs may reduce the efficacy of nivolumab, and their use should be carefully considered in patients receiving nivolumab.},
}

@article {pmid40227849,
year = {2025},
author = {Caussy, C and Rieusset, J and Koppe, L},
title = {The Gut Microbiome and the Gut-Liver-Kidney Axis in Metabolic-Associated Steatotic Liver Disease and Chronic Kidney Disease.},
journal = {Clinical journal of the American Society of Nephrology : CJASN},
volume = {},
number = {},
pages = {},
doi = {10.2215/CJN.0000000732},
pmid = {40227849},
issn = {1555-905X},
}

@article {pmid40227848,
year = {2025},
author = {Ulsamer, A and Bonilla, S and Pérez-Fernández, X and Rello, J and Sabater-Riera, J},
title = {The pathogenesis of ventilator-associated pneumonia: old and new mechanisms.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2493366},
pmid = {40227848},
issn = {1747-6356},
abstract = {INTRODUCTION: Ventilator-associated pneumonia (VAP), defined as a lung infection that occurs in patients after 48 hours on mechanical ventilation, is among the most frequently found nosocomial infections in intensive care units around the world and is associated with increased morbidity, mortality, and economic burden.

AREAS COVERED: We review the classical mechanisms of VAP development and explore more recent ones, such as dysbiosis, which has changed our view of the pathogenesis of the disease; whereas in the past the lower respiratory tract was classically considered a sterile organ, the use of new diagnostic techniques has shown that the lungs of healthy humans are inhabited by a large, dynamic ecosystem of microorganisms. Dysbiosis is the disruption of this ecosystem and is a key factor in the development of VAP. Recent findings have demonstrated that host immunity is microbiome-regulated and, consequently, is profoundly affected by dysbiosis. In this paper the significance of the microbiome-immunity crosstalk in the pathophysiology of VAP will be discussed.

EXPERT OPINION: A deeper understanding of mechanisms of VAP pathogenesis should help to devise new preventive, diagnostic and therapeutic strategies for reducing the incidence of this condition and for improving patient prognosis.},
}

@article {pmid40227841,
year = {2025},
author = {Kim, K and Lee, M and Shin, Y and Lee, Y and Kim, TJ},
title = {Optimizing Cancer Treatment Through Gut Microbiome Modulation.},
journal = {Cancers},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/cancers17071252},
pmid = {40227841},
issn = {2072-6694},
support = {2022R1A2C1092956//National Research Foundation of Korea/ ; },
abstract = {The gut microbiome plays a pivotal role in modulating cancer therapies, including immunotherapy and chemotherapy. Emerging evidence demonstrates its influence on treatment efficacy, immune response, and resistance mechanisms. Specific microbial taxa enhance immune checkpoint inhibitor efficacy, while dysbiosis can contribute to adverse outcomes. Chemotherapy effectiveness is also influenced by microbiome composition, with engineered probiotics and prebiotics offering promising strategies to enhance drug delivery and reduce toxicity. Moreover, microbial metabolites, such as short-chain fatty acids, and engineered microbial systems have shown potential to improve therapeutic responses. These findings underscore the importance of personalized microbiome-based approaches in optimizing cancer treatments.},
}

@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 {pmid40227699,
year = {2025},
author = {Manini, C and Larrinaga, G and Angulo, JC and López, JI},
title = {Hot Spots in Urogenital Basic Cancer Research and Clinics.},
journal = {Cancers},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/cancers17071173},
pmid = {40227699},
issn = {2072-6694},
abstract = {Urogenital cancer is very common in the male population of Western countries, a problem of major concern for public health systems, and a frequent test subject for oncological research. In this narrative, we identify the main hot topics for clinics and the basic science of urological cancer in the last few years (from 2021 onwards), considering the information given in the abstracts of almost 300 original articles published in outstanding journals of pathology, urology, and basic science. Once defined, for the top ten list of hot topics (the 2022 WHO update on the classification of urinary and male genital tumors, new entities in kidney cancer, urinary cancer-omics, update on the Gleason grading system, targeted therapies and other novel therapies in renal cancer, news on non-muscle invasive urothelial carcinoma, artificial intelligence in urologic cancer, intratumor heterogeneity influence in therapeutic failures in urologic neoplasms, intratumor microbiome and its influence in urologic tumor aggressiveness, and ecological principles and mathematics applied to urogenital cancer study), each issue is independently reviewed in an attempt to put together the most relevant updates and/or useful features accompanied by selected illustrations. This review article addresses some of the most interesting and current hot spots in urogenital basic cancer research and clinics and is mainly aimed toward clinicians, including pathologists, urologists, and oncologists. Readers are invited to explore each topic for further, more detailed information, in addition to the references provided.},
}

@article {pmid40227635,
year = {2025},
author = {Menon, A and Mutalik, VS and Chen, Y and Ponamgi, S and Peela, S and Schroth, RJ and Ghavami, S and Chelikani, P},
title = {Beyond Genetics: Exploring Lifestyle, Microbiome, and Social Determinants in Oral Cancer Development.},
journal = {Cancers},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/cancers17071094},
pmid = {40227635},
issn = {2072-6694},
abstract = {Oral cancer refers to cancers originating in the oral cavity and oropharyngeal regions. It is the 16th most prevalent cancer and the sixth leading cause of cancer-related deaths. However, the mechanisms of its progression are still being understood, and interventions to provide early diagnosis need to be improved. More studies have recently been conducted on oral cancer, and many reviews have summarized the findings in this field, focusing on individual factors. However, few review articles have evaluated the combinational impacts of different factors on oral cancer. This review aimed to provide an overview of the combinational effects of three extracellular factors, including lifestyle habits, oral microbiome, and socioeconomic factors, on oral cancer progression. Oral cancer is differentially affected by lifestyle habits; high-sugar diets, processed foods, alcohol, smoking, and possibly sleep disorders benefit its progression, whereas eating natural diets, such as fruits, vegetables, fish, and garlic, drinking tea or coffee, and physical exercise can combat it. The oral microbiome could suppress or promote oral cancer progression. Low socioeconomic status can impact oral cancer development. Furthermore, crosstalk among these three factors affects oral cancer progression. This review has limitations in not including all oral cancer-affecting factors and all important publications. More focus should be placed on the combinational effects of multiple factors on oral cancer progression and treatment. The findings in this study could update researchers on the landscape of oral cancer progression and help formulate approaches to promote oral cancer prevention and treatment.},
}

@article {pmid40227389,
year = {2025},
author = {Teymouri, S and Pourhajibagher, M and Bahador, A},
title = {The relationship between the skin microbiome and probiotics in the healing of burn injuries.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40227389},
issn = {1874-9356},
abstract = {The relationship between the skin microbiome and probiotics in the healing of burn injuries has garnered significant attention in recent years. Burn injuries disrupt the delicate balance of the skin microbiome, leading to complications in the healing process. Probiotic therapies have emerged as promising interventions to restore microbial balance, inhibit biofilm formation, and accelerate tissue repair. Probiotics may also mitigate the risk of antibiotic-resistant infections, which is a major concern in burn units. By enhancing immune responses and stimulating the production of antimicrobial peptides, probiotics can effectively combat bacterial colonization and prevent the emergence of drug-resistant strains. A combination of probiotics with other therapies, such as phages or nanoparticles, holds significant promise for enhancing burn healing. This approach can effectively treat burn wounds by promoting wound healing synergy, preventing infection, modulating the immune response, and disrupting biofilms. Overall, the relationship between the skin microbiome and probiotics in burn wound healing has substantial potential to advance the field of burn wound management.},
}

@article {pmid40227324,
year = {2025},
author = {Kiouri, DP and Batsis, GC and Mavromoustakos, T and Giuliani, A and Chasapis, CT},
title = {Structure-Based Modeling of the Gut Bacteria-Host Interactome Through Statistical Analysis of Domain-Domain Associations Using Machine Learning.},
journal = {Biotech (Basel (Switzerland))},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biotech14010013},
pmid = {40227324},
issn = {2673-6284},
abstract = {The gut microbiome, a complex ecosystem of microorganisms, plays a pivotal role in human health and disease. The gut microbiome's influence extends beyond the digestive system to various organs, and its imbalance is linked to a wide range of diseases, including cancer and neurodevelopmental, inflammatory, metabolic, cardiovascular, autoimmune, and psychiatric diseases. Despite its significance, the interactions between gut bacteria and human proteins remain understudied, with less than 20,000 experimentally validated protein interactions between the host and any bacteria species. This study addresses this knowledge gap by predicting a protein-protein interaction network between gut bacterial and human proteins. Using statistical associations between Pfam domains, a comprehensive dataset of over one million experimentally validated pan-bacterial-human protein interactions, as well as inter- and intra-species protein interactions from various organisms, were used for the development of a machine learning-based prediction method to uncover key regulatory molecules in this dynamic system. This study's findings contribute to the understanding of the intricate gut microbiome-host relationship and pave the way for future experimental validation and therapeutic strategies targeting the gut microbiome interplay.},
}

@article {pmid40227282,
year = {2025},
author = {Villella, VR and Castaldo, A and Scialò, F and Castaldo, G},
title = {How Effectively Can Oxidative Stress and Inflammation Be Reversed When CFTR Function Is Pharmacologically Improved?.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antiox14030310},
pmid = {40227282},
issn = {2076-3921},
abstract = {A critical challenge in the age of advanced modulator therapies is to understand and determine how effectively chronic oxidative stress and oxidative stress-induced inflammation can be reversed and physiological balance restored when CFTR function is pharmacologically improved. The triple therapy with elexacaftor-tezacaftor-ivacaftor (ETI) suggests that CFTR activity in individuals with at least one F508del mutation can be partially restored to about 50% of normal levels. Although incomplete, the partial recovery of CFTR function has been shown to drastically lower sputum pathogen content, enhance microbiome diversity, and lower inflammation markers within the first year of treatment in adolescents and adults with cystic fibrosis. However, despite these advancements, residual airway infection, oxidative stress and inflammation persist, with levels similar to other chronic lung conditions, like non-CF bronchiectasis. This persistence highlights the necessity for innovative antioxidant and anti-inflammatory treatments, in particular for individuals with advanced lung disease. To address this issue, emerging multi-omics technologies offer valuable tools to investigate the impact of modulator therapies on various molecular pathways. By analyzing changes in gene expression, epigenetic modifications, protein profiles and metabolic processes in airway-derived samples, it could be possible to uncover the mechanisms driving persistent oxidative stress and inflammation. These insights could pave the way for identifying new therapeutic targets to fully restore airway health and overall physiological balance.},
}

@article {pmid40227262,
year = {2025},
author = {García Mansilla, MJ and Rodríguez Sojo, MJ and Lista, AR and Ayala Mosqueda, CV and Ruiz Malagón, AJ and Ho Plagaro, A and Gálvez, J and Rodríguez Nogales, A and Rodríguez Sánchez, MJ},
title = {Microbial-Derived Antioxidants in Intestinal Inflammation: A Systematic Review of Their Therapeutic Potential.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/antiox14030321},
pmid = {40227262},
issn = {2076-3921},
support = {CTS 164//Junta de Andalucia/ ; PY20-01157//Junta de Andalucia/ ; B-CTS-664-UGR20//Fondo Europeo de Desarrollo Regional (FEDER)/ ; PI19/01058//Instituto de Salud Carlos III/ ; PI24/02089//Instituto de Salud Carlos III/ ; },
abstract = {The potential of microbial-derived antioxidants to modulate intestinal inflammation is increasingly recognized, which is especially important in inflammatory bowel diseases (IBD). Oxidative stress, a major contributor to chronic intestinal inflammation, is the result of an imbalance between the production of reactive oxygen species (ROS) and the body's antioxidant defenses. This systematic review explores the role of microbial-derived antioxidants in alleviating IBD. Among the main findings are certain compounds, such as exopolysaccharides (EPS) and short-chain fatty acids (SCFAs), which have demonstrated their ability to neutralize ROS and strengthen the integrity of the intestinal barrier, thereby attenuating inflammatory responses. These antioxidants offer the dual benefit of mitigating oxidative stress and rebalancing the gut microbiota, which is often disrupted in IBD. Evidence from preclinical and clinical studies provides a better understanding of the mechanisms involved in the effects of these microbial antioxidants. Conventional treatments for IBD primarily focus on immune modulation. In this context, the integration of microbial-derived antioxidants could offer a complementary approach by addressing both oxidative damage and gut dysbiosis. Further research and clinical trials are essential to establish standardized treatment guidelines and clarify the long-term efficacy of these promising therapeutic agents.},
}

@article {pmid40227158,
year = {2025},
author = {Zhang, L and Ding, Z and Cui, J and Zhou, X and Yi, N},
title = {Bayesian Generalized Linear Models for Analyzing Compositional and Sub-Compositional Microbiome Data via EM Algorithm.},
journal = {Statistics in medicine},
volume = {44},
number = {7},
pages = {e70084},
doi = {10.1002/sim.70084},
pmid = {40227158},
issn = {1097-0258},
mesh = {Bayes Theorem ; *Algorithms ; Humans ; Linear Models ; *Microbiota ; Computer Simulation ; Monte Carlo Method ; Markov Chains ; },
abstract = {The study of compositional microbiome data is critical for exploring the functional roles of microbial communities in human health and disease. Recent advances have shifted from traditional log-ratio transformations of compositional covariates to zero constraint on the sum of the corresponding coefficients. Various approaches, including penalized regression and Markov Chain Monte Carlo (MCMC) algorithms, have been extended to enforce this sum-to-zero constraint. However, these methods exhibit limitations: penalized regression yields only point estimates, limiting uncertainty assessment, while MCMC methods, although reliable, are computationally intensive, particularly in high-dimensional data settings. To address the challenges posed by existing methods, we proposed Bayesian generalized linear models for analyzing compositional and sub-compositional microbiome data. Our model employs a spike-and-slab double-exponential prior on the microbiome coefficients, inducing weak shrinkage on large coefficients and strong shrinkage on irrelevant ones, making it ideal for high-dimensional microbiome data. The sum-to-zero constraint is handled through soft-centers by applying prior distribution on the sum of compositional or subcompositional coefficients. To alleviate computational intensity, we have developed a fast and stable algorithm incorporating expectation-maximization (EM) steps into the routine iteratively weighted least squares (IWLS) algorithm for fitting GLMs. The performance of the proposed method was assessed by extensive simulation studies. The simulation results show that our approach outperforms existing methods with higher accuracy of coefficient estimates and lower prediction error. We also applied the proposed method to one microbiome study to find microorganisms linked to inflammatory bowel disease (IBD). The methods have been implemented in a freely available R package BhGLM https://github.com/nyiuab/BhGLM.},
}

Bayes Theorem
*Algorithms
Humans
Linear Models
*Microbiota
Computer Simulation
Monte Carlo Method
Markov Chains

@article {pmid40226967,
year = {2025},
author = {Sheehan, DH and Asam, K and Knight, ND and Patel, JJ and Stewart, JA and Molina, PA and Yi, N and Viet, CT and Aouizerat, B and Silver, N and Panuganti, B and Thomas, CM},
title = {Altered Bacteria Abundance Is Associated With Outcomes in Head and Neck Squamous Cell Carcinoma.},
journal = {Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1002/ohn.1262},
pmid = {40226967},
issn = {1097-6817},
abstract = {OBJECTIVE: To determine if microbiome differences exist in head and neck squamous cell carcinoma (HNSCC) based on high-risk pathologic features, smoking, and outcomes using The Cancer Microbiome Atlas (TCMA).

STUDY DESIGN: Database study.

SETTING: Database review.

METHODS: TCMA is a publicly available database containing curated, decontaminated microbial profiles for tumors from 1772 patients. The data were limited to microbiome profiles, survival, and clinicopathologic features for HNSCC patients. Phyloseq objects were created, low-read samples were removed, and differential abundance analysis (DAA) using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) was performed. Statistical analysis was done in R (v4.3.1).

RESULTS: One hundred fifty-six patients with HNSCC were included from TCMA with a mean age of 59 (std 13, min 19, and max 90), 72% male (n = 113), and 91% white (n = 140). Primary sites encompassed oral cavity (n = 106, 68%), oropharynx (n = 26, 17%), and larynx/hypopharynx (n = 24, 15%). For all HNSCC in TCMA, rates of lymphovascular invasion were 17% (n = 26), perineural invasion, 34% (n = 53), and microscopic or gross extranodal extension (ENE), 19% (n = 30). DAA revealed significant changes in bacterial genera based on high-risk pathologic features, smoking status, vital status, and disease-specific survival (DSS). Genera observed with ANCOM-BC2 include Scardovia, Alloscardovia, Lactobacillus, and Corynebacterium genera for vital status and DSS.

CONCLUSION: Changes in the relative abundance of select intratumoral bacterial genera are associated with adverse pathologic features, DSS, and vital status in HNSCC. Shifts in the microbiome need further investigation to determine if they can provide any mechanistic insight or predictive role.},
}

@article {pmid40226712,
year = {2024},
author = {Zhang, Y and Gan, X and Zhou, C and Ye, Z and He, P and Liu, M and Zhang, Y and Yang, S and Qin, X},
title = {Relationship of Regular Laxative Use, Genetic Susceptibility of Depression, and Risk of Incident Depression in the General Population.},
journal = {Depression and anxiety},
volume = {2024},
number = {},
pages = {6863037},
pmid = {40226712},
issn = {1520-6394},
mesh = {Humans ; *Laxatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; *Genetic Predisposition to Disease ; Incidence ; Aged ; Adult ; United Kingdom/epidemiology ; Prospective Studies ; *Depressive Disorder/epidemiology/genetics ; *Depression/epidemiology/genetics ; Follow-Up Studies ; Risk Factors ; },
abstract = {Background: The relationship between laxative use and the risk of depression remains uncertain. We aimed to assess the prospective association of regular laxative use with the risk of incident depression and to examine whether genetic risk of depression modifies this association. Methods: Four hundred fifty thousand forty-five participants without depression at baseline and have complete information on laxative use from the UK Biobank were included. The study outcome was incident depression, derived from linkage to primary care records, hospital inpatient data, death register records, or self-reported medical conditions at follow-up visits. Results: During a median follow-up of 12.4 years, 18,651(4.1%) participants have developed depression. Regular laxative use was significantly associated with a higher risk of incident depression (vs. nonregular laxative use; adjusted hazard ratio [HR] = 1.78, 95% confidence interval [CI], 1.68-1.89). Genetic risk of depression did not significantly modify this association. The risk of incident depression increased with increasing types of laxatives used, with a HR of 1.89 (95%CI, 1.73-2.08) for use of single laxative type and 2.32 (95%CI, 1.82-2.96) for combined use of two or more laxative types (P for trend <0.001). The positive association between regular laxative use and incident depression was more pronounced in men (adjusted HR = 2.21, 95%CI, 1.96-2.48) versus women (adjusted HR = 1.67, 95%CI, 1.56-1.79; P interaction <0.001). Compared to those who did not use laxatives regularly and did not have constipation, participants who used laxatives regularly and had constipation had the highest risk of incident depression (adjusted HR = 2.33, 95%CI, 1.94-2.80). Conclusions: Regular laxative use was significantly associated with a higher risk of incident depression, especially in men.},
}

Humans
*Laxatives/adverse effects/therapeutic use
Male
Female
Middle Aged
*Genetic Predisposition to Disease
Incidence
Aged
Adult
United Kingdom/epidemiology
Prospective Studies
*Depressive Disorder/epidemiology/genetics
*Depression/epidemiology/genetics
Follow-Up Studies
Risk Factors

@article {pmid40226542,
year = {2025},
author = {Cao, J and Wang, S and Ding, R and Liu, Y and Yuan, B},
title = {Comparative analyses of the gut microbiome of two sympatric rodent species, Myodes rufocanus and Apodemus peninsulae, in northeast China based on metagenome sequencing.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19260},
pmid = {40226542},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; China ; *Arvicolinae/microbiology ; *Murinae/microbiology ; *Metagenome ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Proteobacteria/genetics/isolation & purification ; Firmicutes/genetics/isolation & purification ; Sympatry ; Bacteroidetes/genetics/isolation & purification ; },
abstract = {The gut microbiota is integral to an animal's physiology, influencing nutritional metabolism, immune function, and environmental adaptation. Despite the significance of gut microbiota in wild rodents, the Korean field mouse (Apodemus peninsulae) and the gray red-backed vole (Myodes rufocanus) remain understudied. To address this, a metagenomic sequencing analysis of the gut microbiome of these sympatric rodents in northeast China's temperate forests was conducted. Intestinal contents were collected from A. peninsulae and M. rufocanus within the Mudanfeng National Nature Reserve. High-throughput sequencing elucidated the gut microbiome's composition, diversity, and functional pathways. Firmicutes, Bacteroidetes, and Proteobacteria were identified as the dominant phyla, with M. rufocanus showing greater microbiome diversity. Key findings indicated distinct gut bacterial communities between the species, with M. rufocanus having a higher abundance of Proteobacteria. The gut microbiota of A. peninsulae and M. rufocanus differed marginally in functional profiles, specifically in the breakdown of complex carbohydrates, which might reflect their distinct food preferences albeit both being herbivores with a substantial dietary overlap. The investigation further elucidated gut microbiota's contributions to energy metabolism and environmental adaptation mechanisms. This study aligns with information on rodent gut microbiota in literature and highlights the two understudied rodent species, providing comparative data for future studies investigating the role of gut microbiota in wildlife health and ecosystem functioning.},
}

Animals
*Gastrointestinal Microbiome/genetics
China
*Arvicolinae/microbiology
*Murinae/microbiology
*Metagenome
Metagenomics
High-Throughput Nucleotide Sequencing
Proteobacteria/genetics/isolation & purification
Firmicutes/genetics/isolation & purification
Sympatry
Bacteroidetes/genetics/isolation & purification

@article {pmid40226103,
year = {2025},
author = {Meurens, F and Huan, S and Liu, WC and Zhu, L and Liu, W},
title = {Editorial: Exploring the influence of gut microbiome on human health: mechanistic insights from pig models.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570451},
pmid = {40226103},
issn = {1664-302X},
}

@article {pmid40226098,
year = {2025},
author = {Wang, M and Yuan, T and Chen, J and Yang, J and Pu, J and Lin, W and Dong, K and Zhang, L and Yuan, J and Zheng, H and Sun, Y and Xu, J},
title = {A species-level identification pipeline for human gut microbiota based on the V3-V4 regions of 16S rRNA.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1553124},
pmid = {40226098},
issn = {1664-302X},
abstract = {16S rRNA gene sequencing is pivotal for identifying bacterial species in microbiome studies, especially using the V3-V4 hypervariable regions. A fixed 98.5% similarity threshold is often applied for species-level identification, but this approach can cause misclassification due to varying thresholds among species. To address this, our study integrated data from SILVA, NCBI, and LPSN databases, extracting V3-V4 region sequences and supplementing them with 16S rRNA sequences from 1,082 human gut samples. This resulted in a non-redundant amplicon sequence variants (ASVs) database specific to the V3-V4 regions (positions 341-806). Utilizing this database, we identified flexible classification thresholds for 674 families, 3,661 genera, and 15,735 species, finding clear thresholds for 87.09% of families and 98.38% of genera. For the 896 most common human gut species, we established precise taxonomic thresholds. To leverage these findings, we developed the asvtax pipeline, which applies flexible thresholds for more accurate taxonomic classification, notably improving the identification of new ASVs. The asvtax pipeline not only enhances the precision of species-level classification but also provides a robust framework for analyzing complex microbial communities, facilitating more reliable ecological and functional interpretations in microbiome research.},
}

@article {pmid40225900,
year = {2025},
author = {Hoffbeck, C and Middleton, DMRL and Nelson, NJ and Taylor, MW},
title = {Season, Body Condition and Developmental Stage Influence the Gut Microbiota of the Sole Living Rhynchocephalian Reptile (Sphenodon punctatus).},
journal = {Ecology and evolution},
volume = {15},
number = {4},
pages = {e71068},
pmid = {40225900},
issn = {2045-7758},
abstract = {Seasonality plays a crucial role for many species, especially reptiles. In multiple reptile species, seasonality has been linked to shifts in the gut microbiota, influenced by factors, such as ambient temperature, food availability and shifting host function across different seasons. We tested whether the tuatara, an endemic New Zealand reptile and the sole extant member of the order Rhynchocephalia, maintains a stable gut microbiota over 2 years of sampling across three seasons (summer, autumn, spring) or if the dominant bacterial community varies with season. We found that community diversity changed significantly seasonally, with the most diverse gut community found in the spring. We also found that season significantly influenced beta-diversity, as did tuatara developmental stage, tuatara body condition and tick abundance. However, there was little evidence for a recurring seasonal bacterial assemblage in 2024 compared with 2023. For tuatara where the same individual was resampled over multiple seasons, bacterial community composition appeared to be most correlated with the time of sampling, with closer temporal samples more similar to one another than samples taken further apart, which was also seen in the significance of the sampling period as a factor explaining variation across all tuatara. We identified bacterial genera that significantly increased or decreased in each season. Despite notable shifts among seasons, particularly in autumn, the tuatara gut microbiota exhibits remarkable persistence over time, including within individuals.},
}

@article {pmid40225487,
year = {2025},
author = {Wang, K and Liu, Z and Tang, R and Sha, Y and Wang, Z and Chen, Y and Chen, G},
title = {Gallstones in the Era of Metabolic Syndrome: Pathophysiology, Risk Prediction, and Management.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e80541},
pmid = {40225487},
issn = {2168-8184},
abstract = {Gallstone disease (GSD) and metabolic syndrome (MetS) are increasingly prevalent conditions with significant global health implications. Recent evidence highlights a strong epidemiological association between these disorders, driven by shared pathophysiological mechanisms. This review provides a comprehensive analysis of the intricate relationship between MetS and GSD, focusing on the role of insulin resistance, dyslipidemia, obesity, and gut microbiota dysbiosis in gallstone formation. An integrated pathophysiological model is proposed, linking metabolic disturbances to bile cholesterol supersaturation, gallbladder dysmotility, and chronic inflammation. The review also explores clinical implications, including risk prediction models based on metabolic parameters, early detection biomarkers, and targeted interventions such as lifestyle modifications, pharmacological therapies, and microbiome modulation. By addressing the metabolic underpinnings of GSD, this synthesis offers a foundation for developing preventive and therapeutic strategies to mitigate the burden of these interconnected conditions. Future research directions are outlined to refine mechanistic insights and improve clinical outcomes.},
}

@article {pmid40225478,
year = {2025},
author = {Kadam, O and Dalai, S and Chauhan, B and Guru, RR and Mitra, S and Raytekar, N and Kumar, R},
title = {Nanobiotechnology Unveils the Power of Probiotics: A Comprehensive Review on the Synergistic Role of Probiotics and Advanced Nanotechnology in Enhancing Geriatric Health.},
journal = {Cureus},
volume = {17},
number = {3},
pages = {e80478},
pmid = {40225478},
issn = {2168-8184},
abstract = {The geriatric population, comprising ages 65 and above, encounters distinct health obstacles because of physiological changes and heightened vulnerability to diseases. New technologies are being investigated to tackle the intricate health requirements of this population. Recent advancements in probiotics and nanotechnology offer promising strategies to enhance geriatric health by improving nutrient absorption, modulating gut microbiota, and delivering targeted therapeutic agents. Probiotics play a crucial role in maintaining gut homeostasis, reducing inflammation, and supporting metabolic functions. However, challenges such as limited viability and efficacy in harsh gastrointestinal conditions hinder their therapeutic potential. Advanced nanotechnology can overcome these constraints by enhancing the efficacy of probiotics through nano-encapsulation, controlled delivery, and improvement of bioavailability. This review explores the synergistic potential of probiotics and advanced nanotechnology in addressing age-related health concerns. It highlights key developments in probiotic formulations, nano-based delivery systems, and their combined impact on gut health, immunity, and neuroprotection. The convergence of probiotics and nanotechnology represents a novel and transformative approach to promoting healthy aging, paving the way for innovative therapeutic interventions.},
}

@article {pmid40225325,
year = {2025},
author = {Tan, F and Zheng, Y and Wang, C and Huang, J and Liu, X and Su, W and Chen, X and Yang, Z},
title = {Effects of Chenpi Jiaosu on serum metabolites and intestinal microflora in a dyslipidemia population: a randomized controlled pilot trial.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1552117},
pmid = {40225325},
issn = {1664-2392},
mesh = {Humans ; Male ; Female ; *Dyslipidemias/drug therapy/blood/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Double-Blind Method ; Middle Aged ; Adult ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; Aged ; Triglycerides/blood ; Medicine, Chinese Traditional ; },
abstract = {INTRODUCTION: Dyslipidemia is a critical risk factor for atherosclerosis and cardiovascular/cerebrovascular events, necessitating effective long-term management. However, conventional lipid-lowering drugs such as statins and fibrates are limited by adverse effects, including hepatotoxicity and myopathy, which restrict their prolonged use. Traditional Chinese medicine (TCM) and natural health products offer potential alternatives with multi-target mechanisms and improved safety profiles. Tangerine Peel Enzyme Drink (CPJS), a fermented health product derived from tangerine peel, has demonstrated lipid-modulating properties. This study aimed to evaluate the efficacy and safety of CPJS in improving dyslipidemia and explore its underlying metabolic and microbiological mechanisms.

METHODS: A randomized, double-blind, parallel-controlled clinical trial was conducted with 72 participants (55 completers). Participants were divided into CPJS and control groups, receiving an 8-week intervention. Primary outcomes included changes in body weight and serum triglycerides (TG), while safety was assessed via liver/kidney function, creatine kinase, blood, and urine tests. Serum metabolomics (93 differential metabolites identified) and intestinal microbiota analysis were performed to elucidate metabolic pathways and microbial shifts. KEGG enrichment analysis mapped metabolites to biological pathways, such as lipid and amino acid metabolism.

RESULTS: The CPJS group exhibited significant reductions in body weight and TG levels post-intervention (p < 0.05), with no adverse effects observed in safety biomarkers. Metabolomic profiling revealed alterations in fatty acyl, glycerophospholipid, and organic acid metabolites, indicating CPJS modulates lipid metabolism and energy homeostasis. KEGG analysis linked these changes to pathways including triglyceride degradation and amino acid metabolism. Additionally, CPJS increased specific gut microbial taxa associated with lipid regulation, suggesting a microbiome-mediated mechanism.

DISCUSSION: CPJS demonstrates efficacy in improving dyslipidemia through dual mechanisms: direct modulation of triglyceride metabolism and indirect regulation via gut microbiota. Its safety profile aligns with findings from natural products like Cyclocarya paliurus and tempeh, which mitigate lipid abnormalities without hepatotoxicity. The multi-target action of CPJS mirrors TCM principles, where compounds like quercetin and flavonoids in CPJS may synergistically inhibit cholesterol synthesis and enhance lipid clearance. However, further research is needed to isolate active components and validate microbial contributions. Compared to synthetic drugs, CPJS offers a safer adjunct therapy, addressing limitations of current pharmacotherapies. Future studies should explore dose-response relationships and long-term outcomes in diverse populations.},
}

Humans
Male
Female
*Dyslipidemias/drug therapy/blood/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Double-Blind Method
Middle Aged
Adult
*Drugs, Chinese Herbal/therapeutic use/pharmacology
Aged
Triglycerides/blood
Medicine, Chinese Traditional

@article {pmid40225043,
year = {2025},
author = {Zhang, L and Li, X and Shi, L and Zheng, Y and Ding, Y and Yuan, T and Hu, S and Chen, J and Xiao, P},
title = {Bacterial diversity and biomarkers screening of station and carriage surface in Shanghai metro system, China.},
journal = {Current research in microbial sciences},
volume = {8},
number = {},
pages = {100374},
pmid = {40225043},
issn = {2666-5174},
abstract = {BACKGROUND: Mass transit environments, such as the metro, can facilitate the spread of bacteria between humans and their surroundings. These environments are particularly important for human health due to their potential for spreading pathogens and their impact on large populations. To gain a deeper understanding of bacterial distribution in subways, it is essential to identify variables that affect bacterial composition and microorganisms that are probably harmful to human heath.

METHODS: We conducted high-throughput 16S rRNA gene sequencing on surface samples from 5 subway stations in Shanghai, China, during the warm(summer), cold(winter) and transition(autumn) seasons. Bacteria community features across the three seasons were distinguished using random forest classification analyses, followed by in-depth diversity analyses.

RESULTS: Significant differences were observed in surface bacterial communities across seasons. Highly abundant bacterial groups were generally ubiquitous. Among these highly abundant families and genera, some were unique to surface samples. Notably, the phyla Firmicutes, Proteobacteria, and Actinobacteria were predominant, with total abundances of 32.87 %, 29.41 %, and 16.31 %, respectively. Alpha diversity indices were statistically significant (P < 0.05) among different seasons, with autumn exhibiting significantly higher alpha diversity metrics compared to summer and winter. Beta diversity analysis revealed significant compositional dissimilarities and distinct clustering patterns among the three seasons (P < 0.05). An analysis of similarities (ANOSIM) test results indicated significant differences in bacterial patterns at the phylum, class, order, family, genus levels among the seasons (P < 0.05). Random forest classification analyses identified the top 24 bacterial taxa at the genus level across seasons in the metro system.

CONCLUSIONS: We provided a direct comparison of surface bacterial microbiomes, and a comprehensive survey of seasonal variation in subways using culture-independent methods. Our findings reveal differences in both diversity and abundance of certain taxa across seasons, with 24 top indicator bacterial genera identified. This work serves as a reference for understanding the composition and dynamics of bacterial communities and for biomarker screening in subways, a crucial public space in our increasingly urbanized and interconnected world.},
}

@article {pmid40224947,
year = {2025},
author = {Morou-Bermúdez, E and Guo, K and Morales Morales, J and Ricart, K and Patel, RP and Clemente, JC and Joshipura, K},
title = {Nitrate reduction by salivary bacteria, glucose metabolism, and lifestyle.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2489612},
pmid = {40224947},
issn = {2000-2297},
abstract = {BACKGROUND: Nitrate reductases (NR) expressed in oral bacteria reduce nitrate to nitrite. Depending on the environmental conditions and types of bacteria present nitrite can be further reduced to ammonium via Dissimilatory Nitrate Reduction to Ammonium (DNRA), or alternatively to nitric oxide (NO), which impacts cardiometabolic health.

OBJECTIVE: To evaluate the associations between nitrate reduction by salivary bacteria, clinical markers of glucose metabolism, and lifestyle factors that can modulate the oral environment, potentially impacting DNRA and NR expression.

METHODS: A cross-sectional study was conducted using a convenience sample of 144 participants from the San Juan Overweight Adult Longitudinal Study (SOALS), which includes data on glucose metabolism and lifestyle. DNRA and NR activities were measured in saliva under aerobic or CO2-enriched conditions.

RESULTS: DNRA activity was inversely associated with insulin resistance (HOMA-IR) [aerobic3rd vs.1st tertile: β=-0.48 (-0.81, -0.15); CO2-enriched3rd vs.1st tertile β=-0.42 (-0.68, -0.17)], fasting blood glucose [aerobic3rd vs.1st tertile β=-0.144 (-0.268, -0.019); CO2-enriched3rd vs.1st tertile: β=-0.070 (-0.130, -0.011)], and 2-h glucose [CO2-enriched3rd vs.1st tertileβ=-0.21 (-0.37, -0.04)]. Current smokers had lower DNRA activity than non-smokers under aerobic conditions [β=-1.55 (-2.96, -0.14)], but higher under CO2-enriched conditions [β = 0.93 (0.15, 1.71)]. Toothbrushing frequency (twice/day vs. once/day) was positively associated with DNRA activity under CO2-enriched conditions [β = 4.11 (1.90, 6.32)] and with aerobic NR activity [β = 1.20, (0.14, 2.27)]. Physical activity was inversely associated with aerobic NR [β=-0.01, (-0.022, -0.003)]. Under CO2-enriched conditions NR was inversely associated with the BMI (β=-0.11, p = 0.007). Aerobic NR was higher when sucrose was added to the assays (NADP vs. sucrose β=-0.74, p = 0.02) and positively associated with salivary nitrate levels (β = 0.002, p = 0.002).

CONCLUSIONS: Nitrate reduction by salivary bacteria is inversely associated with insulin resistance and can be modulated by lifestyle factors. This knowledge could lead to the development of novel, non-invasive approaches for monitoring and preventing diabetes progression.},
}

@article {pmid40224660,
year = {2025},
author = {Izadifar, Z and Ingber, DE},
title = {A Human Cervix Chip for Preclinical Studies of Female Reproductive Biology.},
journal = {Bio-protocol},
volume = {15},
number = {7},
pages = {e5262},
pmid = {40224660},
issn = {2331-8325},
abstract = {Pathological conditions of the cervix ranging from cervical cancer to structural dysfunction associated with preterm labor all have limited treatment options. Thus, there is a need for physiologically relevant preclinical models that recapitulate the structure and function of this human organ. Here, we describe a protocol for engineering and studying a highly functional in vitro model of the human cervix that is composed of a commercially available, dual-channel, microfluidic, organ-on-a-chip (Organ Chip) device lined by primary cervical epithelial (CE) cells interfaced across a porous membrane with cervical stromal cells. The provision of dynamic and customized media flow through both the epithelial and stromal compartments results in cell growth and differentiation, including the accumulation of a thick mucus layer overlying the epithelium. The resulting model closely mimics the structure, epithelial barrier, mucus composition and structure, and biochemical properties of the in vivo human cervix, as well as its responsiveness to female hormones, pH, and microbiome. This Cervix Chip protocol also includes noninvasive techniques for longitudinal monitoring of the live 3D tissue model. The Cervix Chip offers a powerful preclinical platform for replicating in vivo cervical physiology, studying disease mechanisms, and facilitating the development of new therapeutics and diagnostics. Key features • Creates a functional and physiologically responsive 3D tissue model of the human cervix including a living epithelial-stromal interface. • Enables longitudinal and endpoint analysis of the epithelial and stromal environment and their respective secretions independently. • Allows extended clinically relevant studies, such as assessment of tissue barrier function and mucus production as well as co-culture with microbiome and pathogens. • Uses a commercially available dual-channel microfluidic chip and automated culture system (Zoë[TM] Culture Module, Emulate Inc., USA).},
}

@article {pmid40224146,
year = {2025},
author = {Mukherjee, A and Leali, NF and Salvetti, E and Torriani, S and Cotter, PD and Mathur, H},
title = {OPTIMATRIX v2.0: Optimised protocol to mitigate microbial blooms in the micro-Matrix bioreactor platform used as an ex vivo human distal colon model.},
journal = {MethodsX},
volume = {14},
number = {},
pages = {103275},
pmid = {40224146},
issn = {2215-0161},
abstract = {We previously reported optimisation of the methodology to mitigate Escherichia coli blooms and associated loss of microbial diversity when using the micro-Matrix bioreactor platform as an ex vivo model of the human distal colon. Here, we provide further critical insights that we have gained in this regard through follow-up experiments. We tested four separate faecal fermentation media compositions for the purposes of such ex vivo distal colon model experiments and found that the media composition described by MacFarlane et al. is the most suitable for mitigating such microbial blooms, and concurrently, maintaining microbial diversity. We also tested if pooled or individual donor faecal samples were more suitable and found that pooled samples performed better in terms of maintaining gut microbiota diversity in such batch culture model experiments using the micro-Matrix system. Finally, we determined that prolonged experiments, i.e. for durations of up to 96 h, may be warranted with a view to affording particularly fastidious gut microbes an opportunity to grow and compete with their less fastidious counterparts. Essentially, we provide critical insights into:•Optimal faecal fermentation media to minimise blooms and preserve diversity in ex vivo colon model experiments•Optimal faecal inoculum source and duration of experiments.},
}

@article {pmid40223813,
year = {2025},
author = {Alp-Baltakesmez, D and Ertürkmen, P and Bulantekin, Ö},
title = {Diversity and Functional Roles of Microorganisms in Anatolian Black Pine Cone Vinegar Fermentation.},
journal = {Food science & nutrition},
volume = {13},
number = {4},
pages = {e70155},
pmid = {40223813},
issn = {2048-7177},
abstract = {The parts of some pine species are a rich source of bioactive compounds that can be used in various food products. The current work, the physicochemical, bioactive, antimicrobial, sensory, and aromatic properties of traditional vinegar produced from Anatolian Black Pine Cones from different provinces of Turkey were determined, as well as the cultivable microbial diversity and metagenomic analysis. The total phenolic content of the vinegars ranged from 163.88 to 174.79 mg GAE/L. Antioxidant activity, measured via DPPH and ABTS assays, varied among the samples. CnB vinegar, made from Burdur province cones, stood out for its bioactive compounds, including terpenes, acetic acid, ascorbic acid, and the highest α-terpineol content (3.13%). CnB also exhibited the strongest antimicrobial activity, with the largest inhibition zone (44.91 mm) against E. coli type A, while CnM showed the lowest activity. Sensory evaluations favored CnB for its balanced flavor, while CnV was criticized for excessive sharpness, and CnM was deemed too mild. The bacterial microbiome of CnB was predominantly composed of acetic acid bacteria, with an average concentration of 7.36 log CFU/mL in the enumeration of culturable microorganisms. The dominant bacterial taxa at the phyla level included Proteobacteria (72.296%), Firmicutes (22.062%), Bacteroidota (3.665%), followed by Acetobacteraceae (71.47%), Clostridia (13.187%), Bacilli (5.066%), Bacteroidetes (3.665%), and C. negativicutes (3.737%) at the phylum level. The fungal microbiome was mainly represented by Ascomycota (78.717%) and Eukaryota Incertae sedis (15.840%). The findings demonstrate that pine cone vinegar can be employed in a multitude of applications, including food preservation and health promotion.},
}

@article {pmid40223740,
year = {2025},
author = {Li, Y and Bai, R and Zhu, Y and Shi, P and Wang, T and Zhou, D and Zhou, J and Zhu, T and Zhang, X and Gu, R and Ding, X and Chen, H and Wang, X and Zhu, Z},
title = {Genetic variation in gut microbe as a key regulator of host social behavior in C. elegans.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2490828},
doi = {10.1080/19490976.2025.2490828},
pmid = {40223740},
issn = {1949-0984},
mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Social Behavior ; *Genetic Variation ; *Escherichia coli/genetics/classification ; *Behavior, Animal ; },
abstract = {Gut microbiota have been shown to influence the social behaviors of their hosts, while variations in host genetics can affect the composition of the microbiome. Nonetheless, the degree to which genetic variations in microbial populations impact host behavior, as well as any potential transgenerational effects, remains inadequately understood. Utilizing C. elegans as a model organism, we identified 77 strains of E. coli from a total of 3,983 mutants that significantly enhanced aggregation behavior through various neurobehavioral pathways. This discovery underscores a collaborative regulatory mechanism between microbial genetics and host behavior. Notably, we observed that some mutant bacteria might affect social behavior via the mitochondrial pathway. Additionally, the modulation of social behavior has been identified as a heritable trait in offspring. Our results provide a novel perspective on the regulatory role of microbial genetic variation in host behavior, which may have significant implications for human studies and the development of genetically engineered probiotics aimed at enhancing well-being across generations.},
}

Animals
*Caenorhabditis elegans/microbiology/physiology/genetics
*Gastrointestinal Microbiome/genetics
*Social Behavior
*Genetic Variation
*Escherichia coli/genetics/classification
*Behavior, Animal

@article {pmid40223739,
year = {2025},
author = {El Mouzan, M and Savidge, TC and Al Sarkhy, A and Badu, S and Alsaleem, B and Al Mofarreh, M and Almasood, A and Assiri, A},
title = {Gut virome profile in new onset treatment naïve Saudi children with ulcerative colitis.},
journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association},
volume = {},
number = {},
pages = {},
doi = {10.4103/sjg.sjg_24_25},
pmid = {40223739},
issn = {1998-4049},
abstract = {BACKGROUND: Gut microbiome imbalance is well established in ulcerative colitis (UC) in Western populations. Significantly less is known about the gut virome and whether geography impacts the UC-associated microbiome. The aim of this study was to characterize gut bacteriophage changes, as well as to identify phage-bacterial associations that can serve as potential biomarkers of UC.

METHODS: Twenty children with UC and 20 healthy controls were enrolled in the study. Inclusion criteria included newly diagnosed treatment-naïve children with UC with no antibiotic exposure for at least six months prior to sample collection. Deoxyribonucleic acid (DNA) was extracted from stool and rectal biopsies and was processed for shotgun metagenomic sequencing. Bioinformatics and statistical analyses were performed to assess phage diversity and their associations with gut bacteria. Candidate biomarkers were identified using the random forest classifier.

RESULTS: In fecal samples, bacteriophage diversity was not significantly altered, but 72 species were significantly altered in UC, five of which (Salmonella_phage_SEN4, uncultured_crAssphage, Staphylococcus_phage_SPbeta-like, Streptococcus_phage_YMC-2011 and Siphoviridae_u_s) were identified as candidate biomarker signatures.

CONCLUSIONS: We found a significantly altered bacteriophage signature in children with new onset, treatment naïve UC in Saudi children, a Middle Eastern population. These changes differed from previously reported Western UC cases, indicating that demographic bias needs to be considered when developing microbiota-based diagnostics and therapeutic applications for non-Western populations.},
}

@article {pmid40223703,
year = {2025},
author = {Gao, M and Zhang, Q and Chen, B and Lei, C and Xia, Q and Sun, L and Li, T and Zhou, NY and Lu, T and Qian, H},
title = {Global Geographic Patterns of Soil Microbial Degradation Potential for Polycyclic Aromatic Hydrocarbons.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c00306},
pmid = {40223703},
issn = {1520-5851},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are toxic and persistent pollutants that are widely distributed in the environment. PAHs are toxic to microorganisms and pose ecological risks. Bacteria encode enzymes for PAH degradation through specific genes, thereby mitigating PAH pollution. However, due to PAHs' complexity, information on the global degradation potential, diversity, and associated risks of PAH-degrading microbes in soils is lacking. In this study, we analyzed 121 PAH-degrading genes and selected 33 as marker genes to predict the degradation potential within the soil microbiome. By constructing a Hidden Markov Model, we identified 4990 species carrying PAH-degrading genes in 40,039 soil metagenomic assembly genomes, with Burkholderiaceae and Stellaceae emerging as high-potential degraders. We demonstrated that the candidate PAH degraders predominantly emerged in artificial soil and farmland, with significantly fewer present in extreme environments, driven by factors such as average annual rainfall, organic carbon, and human modification of terrestrial systems. Furthermore, we comprehensively quantified the potential risks of each potential host in future practical applications using three indicators (antibiotic resistance genes, virulence factors, and pathogenic bacteria). We found that the degrader Stellaceae has significant application prospects. Our research will help determine the biosynthetic potential of PAH-degrading enzymes globally and further identify potential PAH-degrading bacteria at lower risk.},
}

@article {pmid40223653,
year = {2025},
author = {Saadawi, A and Mair, F and Rosenwald, E and Hoces, D and Slack, E and Kopf, M},
title = {Investigating Polyreactivity of CD4[+] T Cells to the Intestinal Microbiota.},
journal = {European journal of immunology},
volume = {55},
number = {4},
pages = {e202451484},
doi = {10.1002/eji.202451484},
pmid = {40223653},
issn = {1521-4141},
mesh = {Animals ; *CD4-Positive T-Lymphocytes/immunology ; Mice ; *Gastrointestinal Microbiome/immunology ; Epitopes, T-Lymphocyte/immunology ; *Bacteroides thetaiotaomicron/immunology ; Mice, Inbred C57BL ; Interferon-gamma/immunology/metabolism ; Receptors, Antigen, T-Cell/immunology ; Humans ; Antigens, Bacterial/immunology ; Interleukin-17/immunology/metabolism ; Peptide Library ; },
abstract = {Antigen-specific recognition of microbiota by T cells enforces tolerance at homeostasis. Conversely, dysbiosis leads to imbalanced T-cell responses, triggering inflammatory and autoimmune diseases. Despite their significance, the identities of immunogenic microbial antigens remain largely enigmatic. Here, we leveraged a sensitive, unbiased, genome-wide screening platform to identify peptides from Akkermansia muciniphila (AKK) and Bacteroides thetaiotaomicron (BT) recognized by CD4[+] T cells. The platform is based on screening peptide libraries using an NFAT-fluorescence reporter cell line transduced with a retrovirus encoding an MHC-TCR (MCR) hybrid molecule. We discovered several novel epitopes from AKK and BT. T-cell hybridomas reactive to AKK and BT bacteria demonstrated polyreactivity to microbiota-derived peptides in co-cultures with MCR reporter cells. Steady-state T cells recognized these epitopes in an MHC-restricted fashion. Intriguingly, most of the identified epitopes are broadly conserved within the given phylum and originate from membrane and intracellular proteins. Ex vivo stimulation of CD4[+] T cells from mice vaccinated with the identified peptides revealed mono-specific IFN-γ and IL-17 responses. Our work showcases the potential of the MCR system for identifying immunogenic microbial epitopes, providing a valuable resource. Our study facilitates decoding antigen specificity in immune system-bacterial interactions, with applications in understanding microbiome and pathogenic bacterial immunity.},
}

Animals
*CD4-Positive T-Lymphocytes/immunology
Mice
*Gastrointestinal Microbiome/immunology
Epitopes, T-Lymphocyte/immunology
*Bacteroides thetaiotaomicron/immunology
Mice, Inbred C57BL
Interferon-gamma/immunology/metabolism
Receptors, Antigen, T-Cell/immunology
Humans
Antigens, Bacterial/immunology
Interleukin-17/immunology/metabolism
Peptide Library

@article {pmid40223320,
year = {2025},
author = {Yaghmaei, H and Taromiha, A and Nojoumi, SA and Soltanipur, M and Shahshenas, S and Rezaei, M and Mirhosseini, SM and Hosseini, SM and Siadat, SD},
title = {Role of Gut-Liver Axis in Non-Alcoholic Fatty Liver Disease.},
journal = {Iranian biomedical journal},
volume = {29},
number = {1 & 2},
pages = {1-8},
pmid = {40223320},
issn = {2008-823X},
mesh = {*Non-alcoholic Fatty Liver Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; *Liver/pathology/microbiology/metabolism ; Dysbiosis ; },
abstract = {Non-alcoholic fatty liver disease has emerged as a significant global health problem, mainly due to the increasing prevalence of obesity and metabolic syndrome. The gut microbiota plays an essential role in the development of NAFLD through the gut-liver axis. Dysbiosis of the GM is associated with the pathogenesis of NAFLD. Dietary choices and other lifestyle factors influence the composition of the GM and contribute to the development of NAFLD. At the phylum level, individuals with NAFLD show an increased level in Actinobacteria and Firmicutes, while Verrucomicrobia, Thermus, Proteobacteria, Lentiphaerae, and Fusobacteria are found to be decreased. Several genera, including Faecalibacterium and Akkermansia, exhibit alterations in NAFLD and are linked to disease progression. Modulating the GM through prebiotics, probiotics, or fecal microbiota transplantation represents a promising therapeutic strategy for NAFLD. This review summarizes the current understanding of GM changes in NAFLD, focusing on findings from both human and animal studies.},
}

*Non-alcoholic Fatty Liver Disease/microbiology
Humans
*Gastrointestinal Microbiome
Animals
*Liver/pathology/microbiology/metabolism
Dysbiosis

@article {pmid40223273,
year = {2025},
author = {Yang, SY and Han, SM and Lee, JY and Kim, KS and Lee, JE and Lee, DW},
title = {Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412001},
doi = {10.4014/jmb.2412.12001},
pmid = {40223273},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods/trends ; *Metabolomics/methods ; *Genomics/methods ; Proteomics/methods ; Precision Medicine ; Host Microbial Interactions ; Multiomics ; },
abstract = {The gut microbiome, a dynamic and integral component of human health, has co-evolved with its host, playing essential roles in metabolism, immunity, and disease prevention. Traditional microbiome studies, primarily focused on microbial composition, have provided limited insights into the functional and mechanistic interactions between microbiota and their host. The advent of multi-omics technologies has transformed microbiome research by integrating genomics, transcriptomics, proteomics, and metabolomics, offering a comprehensive, systems-level understanding of microbial ecology and host-microbiome interactions. These advances have propelled innovations in personalized medicine, enabling more precise diagnostics and targeted therapeutic strategies. This review highlights recent breakthroughs in microbiome research, demonstrating how these approaches have elucidated microbial functions and their implications for health and disease. Additionally, it underscores the necessity of standardizing multi-omics methodologies, conducting large-scale cohort studies, and developing novel platforms for mechanistic studies, which are critical steps toward translating microbiome research into clinical applications and advancing precision medicine.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods/trends
*Metabolomics/methods
*Genomics/methods
Proteomics/methods
Precision Medicine
Host Microbial Interactions
Multiomics

@article {pmid40223270,
year = {2025},
author = {Jin, YJ and Park, YJ and Choi, J and Kim, MS and Min, U and Lim, J and Kang, J and Lee, DY and Kim, BY},
title = {Impact of Probiotic Formula (Lacto-5X) on Constipation: Improvements in Gastrointestinal Symptoms, Gut Microbiome, and Metabolites.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2412056},
doi = {10.4014/jmb.2412.12056},
pmid = {40223270},
issn = {1738-8872},
mesh = {*Probiotics/therapeutic use/administration & dosage ; *Constipation/microbiology/drug therapy/therapy ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Double-Blind Method ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Metabolome ; Treatment Outcome ; Gastrointestinal Tract/microbiology ; Lactobacillus ; },
abstract = {Constipation is characterized by low frequent stools and difficult stool passage. Approximately 16% of the global population experiences these symptoms. Probiotics have shown promise in improving constipation symptoms by modulating the gut microbiome. This study aims to evaluate the effects of a probiotic formula (Lacto-5X) on bowel habits, gastrointestinal symptoms, gut microbiome, and metabolites in adults with mild constipation using a randomized, double-blind, placebo-controlled clinical trial design. At the 4-week endpoint, the Probiotic group had significant improvements in stool consistency, stool frequency, abdominal pain, and straining compared to the Placebo group. Satisfaction with bowel habits and improvement in overall intestinal health were significantly higher in the Probiotic group. Microbiome analysis revealed a significant increase in the abundance of Lactobacillus and L. plantarum in the Probiotic group at the 4-week endpoint. Metabolome analysis showed that L-proline level in the Probiotic group decreased, while threonic acid level increased at the 4-week endpoint compared to the Placebo group. However, these improvements were not sustained at the 8-week follow-up point. Lacto-5X changes the gut microbiome, leading to changes in metabolites, and it induced improved constipation symptoms. Continuous intake may be necessary to maintain these effects. Further studies are needed to explore the long-term efficacy of Lacto-5X.},
}

*Probiotics/therapeutic use/administration & dosage
*Constipation/microbiology/drug therapy/therapy
Humans
*Gastrointestinal Microbiome/drug effects
Male
Double-Blind Method
Female
Adult
Middle Aged
Feces/microbiology
Metabolome
Treatment Outcome
Gastrointestinal Tract/microbiology
Lactobacillus

@article {pmid40222850,
year = {2025},
author = {Bazacliu, C and Roig, JC and Neu, J},
title = {Gastrointestinal (GI)-lung-brain axis.},
journal = {Seminars in fetal & neonatal medicine},
volume = {},
number = {},
pages = {101639},
doi = {10.1016/j.siny.2025.101639},
pmid = {40222850},
issn = {1878-0946},
abstract = {The GI tract-lung-brain axis refers to the communication network linking the gastrointestinal tract, central nervous system, and respiratory system. This axis is particularly significant in preterm neonates because their immune and nervous systems are undergoing rapid development and thus are susceptible to various conditions influenced by GI tract and lung microbiota that are key mediators in this axis. This communication network is connected via neural, hormonal, and immunological regulatory pathways, all of which are pivotal in disease pathogenesis and health. Here we provide a brief introduction to this axis along with interactive mechanisms and perturbations that can affect this system and the roles they play in health and disease.},
}

@article {pmid40222615,
year = {2025},
author = {Gopalakrishnan, V and Kumar, C and Robertsen, I and Morehouse, C and Sparklin, B and Khader, S and Henry, I and Johnson, LK and Hertel, JK and Christensen, H and Sandbu, R and Greasley, PJ and Sellman, BR and Åsberg, A and Andersson, S and Löfmark, RJ and Hjelmesæth, J and Karlsson, C and Cohen, TS},
title = {A multi-omics microbiome signature is associated with the benefits of gastric bypass surgery and is differentiated from diet induced weight loss through 2 years of follow-up.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.04.002},
pmid = {40222615},
issn = {1935-3456},
abstract = {Roux-en-Y gastric bypass (GBP) surgery is an effective treatment for reducing body weight and correcting metabolic dysfunction in individuals with severe obesity. Herein, we characterize the differences between very low energy diet (VLED) and GBP induced weight loss by multi-omic analyses of microbiome and host features in a non-randomized, controlled, single-center study. Eighty-eight participants with severe obesity were recruited into two arms - GBP versus VLED with matching weight loss for 6 weeks and 2-years of follow-up. A dramatic shift in the distribution of gut microbial taxa and their functional capacity was seen in the GBP group at Week 2 after surgery and was sustained through 2 years. Multi-omic analyses were performed after 6 weeks of matching weight loss between the GBP and VLED groups, which pointed to microbiome derived metabolites such as indoxyl sulphate as characterizing the GBP group. We also identified an inverse association between Streptococcus parasanguinis (an oral commensal) and plasma levels of tryptophan and tyrosine. These data have important implications, as they reveal a significant robust restructuring of the microbiome away from a baseline dysbiotic state in the GBP group. Furthermore, multi-omics modelling points to potentially novel mechanistic insights at the intersection of the microbiome and host.},
}

@article {pmid40222563,
year = {2025},
author = {Thakur, R and Kaur, S},
title = {Use of postbiotics and parabiotics from lactobacilli in the treatment of infectious diarrhea.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107580},
doi = {10.1016/j.micpath.2025.107580},
pmid = {40222563},
issn = {1096-1208},
abstract = {Probiotics are effective in the treatment of diarrheal disease which is the second leading cause of death in children below the age of five years via the production of antimicrobial peptides and lactic acid. These live bacteria are known to benefit the host by modulating their gut microbiome and competitively excluding pathogens from the gut. As probiotics are live microbial cells, their safety evaluation is a concern that shifts the focus from the usage of live cells to parabiotics and postbiotics. In recent years attempts have been made to study the efficacy of postbiotics and parabiotics against enteric pathogens. Enteric pathogens are the major cause of diarrhea resulting in watery stools and electrolyte imbalance. Among various gastrointestinal illnesses, 30% are caused by bacteria. These gastrointestinal infections in adults have usually mild to moderate symptoms that disappear spontaneously but, in some cases, they can cause chronic diseases such as typhoid, irritable bowel syndrome, ulcerative colitis and bacteremia. The extensive use of antibiotics for the treatment of bacterial-infection-induced diarrhea has led to the emergence of drug resistance among these enteric pathogens. Drug resistance poses a major threat in the treatment of various other diseases as well. Further, the use of antibiotics is known to disrupt the homeostasis of the gut by killing the normal gut flora thereby worsening the situation. Therefore, the urgent need for new interventions to combat these enteric pathogens along with restoration of gut barrier. Lactobacillus-derived parabiotics and postbiotics have emerged as promising approaches for managing and treating diarrheal diseases. Therefore, our research is focused on studying the efficacy and underlying mechanisms of Lactobacillus spp.-derived postbiotics and parabiotics against enteric pathogens. Understanding these mechanisms helps in combatting diarrhea associated with enteric pathogens and results in reducing the morbidity and mortality rates associated with infectious diarrhea and its complications.},
}

@article {pmid40229018,
year = {2024},
author = {Chalif, J and Wang, H and Spakowicz, D and Quick, A and Arthur, EK and O'Malley, D and Chambers, LM},
title = {The microbiome and gynecologic cancer: cellular mechanisms and clinical applications.},
journal = {International journal of gynecological cancer : official journal of the International Gynecological Cancer Society},
volume = {34},
number = {2},
pages = {317-327},
doi = {10.1136/ijgc-2023-004894},
pmid = {40229018},
issn = {1525-1438},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/microbiology/therapy ; *Microbiota/physiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; },
abstract = {The microbiome plays a vital function in maintaining human health and homeostasis. Each microbiota has unique characteristics, including those of the gastrointestinal and female reproductive tract. Dysbiosis, or alterations to the composition of the microbial communities, impacts the microbiota-host relationship and is linked to diseases, including cancer. In addition, studies have demonstrated that the microbiota can contribute to a pro-carcinogenic state through altered host immunologic response, modulation of cell proliferation, signaling, gene expression, and dysregulated metabolism of nutrients and hormones. In recent years, the microbiota of the gut and female reproductive tracts have been linked to many diseases, including gynecologic cancers. Numerous pre-clinical and clinical studies have demonstrated that specific bacteria or microbial communities may contribute to the development of gynecologic cancers. Further, the microbiota may also impact the toxicity and efficacy of cancer therapies, including chemotherapy, immunotherapy, and radiation therapy in women with gynecologic malignancies. The microbiota is highly dynamic and may be altered through various mechanisms, including diet, exercise, medications, and fecal microbiota transplantation. This review provides an overview of the current literature detailing the relationship between gynecologic cancers and the microbiota of the female reproductive and gastrointestinal tracts, focusing on mechanisms of carcinogenesis and strategies for modulating the microbiota for cancer prevention and treatment. Advancing our understanding of the complex relationship between the microbiota and gynecologic cancer will provide a novel approach for prevention and therapeutic modulation in the future.},
}

Humans
Female
*Genital Neoplasms, Female/microbiology/therapy
*Microbiota/physiology
*Gastrointestinal Microbiome
Dysbiosis/microbiology

@article {pmid40222540,
year = {2025},
author = {Wang, M and Wang, Y and Wang, X and Qiu, Y and Li, C and Li, H and Li, H and Yu, J},
title = {Lactoferrin ameliorates cognitive impairment in D-galactose-induced aging mice by regulating the PI3K/Akt/mTOR signaling pathway and the microbiome-gut-brain axis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {143033},
doi = {10.1016/j.ijbiomac.2025.143033},
pmid = {40222540},
issn = {1879-0003},
abstract = {Lactoferrin (LF) has been shown to be effective in attenuating oxidative stress, neuroinflammation, but its potential and mechanisms in alleviating brain aging remain to be clarified. In this study, the effect of different doses of LF (L: 50, M: 500 and H: 2000 mg/kg) on D-galactose (D-gal)-induced brain aging C57BL/6 mice was evaluated. The results showed that body weight, mobility, and spatial memory capacity of aging mice were restored after LF (M & H) intervention. It also attenuated hippocampal neuronal damage and intestinal barrier damage in aging mice. LF (M & H) increased brain and serum levels of antioxidant defense enzymes (SOD, GSH, CAT) and decreased colon and serum levels of inflammatory factors (IL-1β, IL-6 and TNF-α). Western blotting results showed that LF (M & H) increased LC3II/I, Beclin1 expression, decreased p-mTOR, p-akt, and p62 expression, and restored autophagy through the PI3K/Akt/m-TOR pathway. Furthermore, LF (M & H) protected the intestinal barrier by regulating the ratio of Firmicutes/Bacteroidetes and increased levels of the beneficial metabolites short chain fatty acids (SCFAs). Notably, LF (H) exhibited the best anti-aging potential. 500 mg/kg/day LF intervention may be cost-effective in prevents brain aging by regulating the autophagy pathway and the microbiome-gut-brain axis.},
}

@article {pmid40222449,
year = {2025},
author = {Alver, SK and Peters-Samuelson, BA and Mossavar-Rahmani, Y and Qi, Q and McClain, AC and Van Horn, L and Burk, RD and Kaplan, RC},
title = {Association of meal timing with adiposity measures and gut microbiome characteristics in a cohort study: the Hispanic Community Health Study/Study of Latinos.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.04.003},
pmid = {40222449},
issn = {1938-3207},
abstract = {BACKGROUND: Time-restricted eating may help control weight through caloric restriction, circadian rhythm, or influence on the gut microbiome (GMB). Physical activity (PA) also plays a role, as people with a longer eating window (EW: time between first and last daily intake) may be more active. The associations between meal timing, adiposity, PA, sedentary behavior (SB) and GMB characteristics are of interest in Hispanic/Latino persons, who experience a high burden of cardiometabolic diseases.

OBJECTIVE: We explored the relationship of EW with energy intake and accelerometer-measured activity and assessed whether a longer EW and later midpoint of intake (MOI: midpoint time of intake) are associated with adiposity and GMB differences in Hispanic/Latino adults.

METHODS: Using data from the prospective Hispanic Community Health Study/Study of Latinos (n=11,778 participants with valid 24-hour dietary recall and accelerometer data, no unplanned weight loss, and BMI ≥18.5; n=1925 with GMB data) we explored the relationship between EW, SB and energy intake. We used multivariable linear regression models to study the relationship between EW or MOI and adiposity measures and GMB characteristics, adjusted for clinical, behavioral, and demographic characteristics.

RESULTS: Those with longer EW tended to have less SB and greater energy intake, suggesting that some individuals may balance greater intake with greater expenditure. After adjustments including energy balance, each hour of EW was associated with 0.29% higher BMI (95% CI 0.07, 0.51), p=0.011. Longer EW and caloric EW (EWC: EW, caloric meals only) were associated with several obesity-associated GMB taxa, such as Streptococcus (enriched, β [95% CI] 0.04 [0.01, 0.07] for EW). MOI was not significantly associated with adiposity or GMB characteristics.

CONCLUSIONS: Shorter EW may promote healthy weight, but some individuals with longer vs shorter EWs tend to have greater activity that could balance their greater energy intake. EW and EWC may influence GMB characteristics.},
}

@article {pmid40222422,
year = {2025},
author = {Qiu, X and Gao, Q and Wang, J and Zhang, Z and Tao, L},
title = {The microbiota-m[6]A-metabolism axis: Implications for therapeutic strategies in gastrointestinal cancers.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189317},
doi = {10.1016/j.bbcan.2025.189317},
pmid = {40222422},
issn = {1879-2561},
abstract = {Gastrointestinal (GI) cancers remain a leading cause of cancer-related mortality worldwide, with metabolic reprogramming recognized as a central driver of tumor progression and therapeutic resistance. Among the key regulatory layers, N[6]-methyladenosine (m[6]A) RNA modification-mediated by methyltransferases (writers such as METTL3/14), RNA-binding proteins (readers like YTHDFs and IGF2BPs), and demethylases (erasers including FTO and ALKBH5), plays a pivotal role in controlling gene expression and metabolic flux in the tumor context. Concurrently, the gut microbiota profoundly influences GI tumorigenesis and immune evasion by modulating metabolite availability and remodeling the tumor microenvironment. Recent evidence has uncovered a bidirectional crosstalk between microbial metabolites and m[6]A methylation: microbiota-derived signals dynamically regulate m[6]A deposition on metabolic and immune transcripts, while m[6]A modifications, in turn, regulate the stability and translation of key mRNAs such as PD-L1 and FOXP3. This reciprocal interaction forms self-reinforcing epigenetic circuits that drive tumor plasticity, immune escape, and metabolic adaptation. In this review, we dissect the molecular underpinnings of the microbiota-m[6]A-metabolism axis in GI cancers and explore its potential to inform novel strategies in immunotherapy, metabolic intervention, and microbiome-guided precision oncology.},
}

@article {pmid40222268,
year = {2025},
author = {Dave, YA and Koperska, M and Lucerne, KE and Shipman, AL and Zeldin, SM and Osman, A and Hofford, RS and Kiraly, DD},
title = {Gut microbiome depletion modulates cocaine-induced behavioral and transcriptional responses in female mice.},
journal = {Journal of neuroimmunology},
volume = {403},
number = {},
pages = {578609},
doi = {10.1016/j.jneuroim.2025.578609},
pmid = {40222268},
issn = {1872-8421},
abstract = {Cocaine use disorder is a chronic relapsing condition with no FDA-approved biological treatments. The gut microbiome has emerged as a key modulator of neurobehavioral responses to drugs of abuse, yet its role in female animals has been under studied. Here, we investigated the effects of gut microbiome depletion on cocaine-induced behavioral and transcriptional responses in female mice. Adult female C57BL/6 J mice were treated with a non-absorbable oral antibiotic (Abx) cocktail for two weeks to deplete the gut microbiome, followed by behavioral assays assessing locomotor sensitization and conditioned place preference (CPP) to cocaine. Abx-treated females displayed reduced locomotor sensitization and a shifted CPP dose-response curve, characterized by attenuated preference at higher cocaine doses. Transcriptional analysis of the nucleus accumbens (NAc) revealed that microbiome depletion suppressed cocaine-induced expression of immediate early genes (c-Fos, FosB, Nr4a1, Egr4) and altered dopamine-related (Drd1) and microglial (Cx3cr1) markers. These findings contrast with prior studies in males, where microbiome depletion enhanced cocaine-induced behavioral plasticity. The observed effects suggest distinct gut-brain signaling as an important contributor to cocaine reinforcement and neuroadaptations in females. This study provides novel insights into microbiome regulation of addiction-relevant behaviors and highlights the necessity of sex-specific investigations in neuropsychiatric disorders. Further research is needed to elucidate the molecular pathways linking gut dysbiosis to substance use vulnerability in females.},
}

@article {pmid40222148,
year = {2025},
author = {Guo, Z and Yang, R and Hua, Z and Long, W and Xiang, Q},
title = {Effect of polystyrene nanoplastics on the intestinal histopathology, oxidative stress, and microbiota of Acrossocheilus yunnanensis.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {283},
number = {},
pages = {107359},
doi = {10.1016/j.aquatox.2025.107359},
pmid = {40222148},
issn = {1879-1514},
abstract = {Even though extensive research exists on the negative impact of nanoplastics on fish, their effect on the microbiota and intestinal health of freshwater fish remains unclear. This study investigated the impact of polystyrene nanoplastics (PS-NPs) on the microbiota, oxidative stress, and intestinal morphology of the Acrossocheilus yunnanensis (A. yunnanensis) freshwater fish species. The findings demonstrated that PS-NPs induced structural changes (e.g., epithelial rupture and microvilli damage) in the intestinal tissue of A. yunnanensis. Meanwhile, they increased the level of malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) in the intestine, but did not significantly cause changes in the activities of catalase (CAT) and glutathione S-transferase (GST) enzymes. The microbiome results indicated that PS-NPs increased gut microbial community diversity and Proteobacteria abundance while decreasing the Fusobacteriota content. Furthermore, PS-NPs significantly improved multiple microbial functions such as amino acid and lipid transfer and metabolism, as well as energy generation and conversion. Overall, this study revealed that PS-NPs caused oxidative stress and microbiota dysbiosis in A. yunnanensis, possibly causing intestinal epithelial damage. This research elucidates the mechanism underlying PS-NP toxicity to freshwater fish and its subsequent impact.},
}

@article {pmid40221798,
year = {2025},
author = {Chiu, L and Guo, JL and Li, HW and Chang, HJ and Yang, SH and Dufour, S and Chang, CF and Tseng, YC and Wu, GC},
title = {Microbial diversity and pigment synthesis in the accessory nidamental gland: species-specific and color-associated patterns in bigfin reef squid (Sepioteuthis lessoniana).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {36},
pmid = {40221798},
issn = {2524-4671},
support = {The Featured Areas Research Center Program within the framework of the Higher Education Sprout Project//Ministry of Education/ ; NSTC 111-2326-B-019-001-MY3//National Science and Technology Council/ ; },
abstract = {BACKGROUND: In certain cephalopod species, two distinct symbiotic organs host large populations of microorganisms: the light organ, regulated by the daily cycle, and the accessory nidamental gland (ANG), regulated by the female reproductive cycle. While host-microbiota interactions in the light organ of the bobtail squid are well understood, the dynamics within the ANG remain largely unexplored. This study uses the bigfin reef squid, Sepioteuthis lessoniana, as a model to investigate the microbiomes associated with specific regions of the ANG, capitalizing on its relatively large gland size compared to the bobtail squid. Our goal was to characterize species-specific microbiomes in the ANG and explore how pigmented region-dependent microbes contribute to reproductive fitness in bigfin reef squid.

RESULTS: Histological results indicate that four types of epithelial cells were observed in the secondary tubules of inner ANG layer. Using an amplicon-based approach, we found that Alphaproteobacteria were highly abundant in different cephalopod species. Beta diversity analyses revealed significant interspecies differences in microbiomes, while alpha diversity showed that the bigfin reef squid harbored a richer bacterial community than the other two species. Notably, pigmented regions of the ANG exhibited lower microbial diversity compared to whole ANG tissues, with Alphaproteobacteria significantly enriched in these regions. Hyphomicrobiaceae (Alphaproteobacteria) were unique to the orange regions, while Fodinicurvataceae (Alphaproteobacteria) and Flavobacteriaceae (Bacteroidia) were exclusive to the white regions. qPCR results showed higher transcription levels of immune response-associated genes in the orange region compared to other pigmented regions, suggesting localized immune interactions.

CONCLUSIONS: These findings suggest that Alphaproteobacteria, particularly the Hyphomicrobiaceae clade, may correlated to the synthesis orange pigmentation in the ANG of the bigfin reef squid. The roles of Hyphomicrobiaceae in ANG symbiosis and reproductive fitness still needs further investigation. With this knowledge, we propose further investigations using in situ hybridization to detect host-expressed genes and pigmented region-dependent bacteria as markers. This approach will facilitate the study of localized host-microbiota interactions in distinct pigmented regions of the ANG, providing deeper insights into the mechanism of host-microbe communication.},
}

@article {pmid40221753,
year = {2025},
author = {Janeckova, L and Stastna, M and Hrckulak, D and Berkova, L and Kubovciak, J and Onhajzer, J and Kriz, V and Dostalikova, S and Mullerova, T and Vecerkova, K and Tenglerova, M and Coufal, S and Kostovcikova, K and Blumberg, RS and Filipp, D and Basler, K and Valenta, T and Kolar, M and Korinek, V},
title = {Tcf4 regulates secretory cell fate decisions in the small intestine and colon tumors: insights from transcriptomic, histological, and microbiome analyses.},
journal = {Stem cell research & therapy},
volume = {16},
number = {1},
pages = {170},
pmid = {40221753},
issn = {1757-6512},
support = {20-31322S//Grantová Agentura České Republiky/ ; LX22NPO5102//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; LM2023055//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; LM2023050//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; RVO - 68378050-KAV-NPUI//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; LQ200202105//Akademie Věd České Republiky/ ; DK088199//Foundation for the National Institutes of Health/ ; },
mesh = {Animals ; *Intestine, Small/metabolism/pathology/microbiology ; Mice ; *Colonic Neoplasms/pathology/genetics/microbiology/metabolism ; Paneth Cells/metabolism ; *Transcriptome ; *Transcription Factor 4/metabolism/genetics ; Humans ; Cell Differentiation ; *Gastrointestinal Microbiome ; Wnt Signaling Pathway ; Organoids/metabolism ; alpha-Defensins/metabolism ; Goblet Cells/metabolism ; },
abstract = {BACKGROUND: The canonical Wnt signaling pathway controls the continuous renewal of the intestinal epithelium and the specification of epithelial cell lineages. Tcf4, a nuclear mediator of Wnt signaling, is essential for the differentiation and maintenance of Paneth cells in the small intestine. Its deficiency is associated with reduced expression of key α-defensins, highlighting its role in host-microbe interactions. However, the exact function of Tcf4 in specifying the secretory lineage and its contribution to antimicrobial peptide production remain incompletely understood. Remarkably, α-defensin expression has also been detected in human colon adenomas, where aberrant Wnt signaling is a hallmark. This raises important questions: What is the role of these Paneth-like cells in tumor biology, and how does Tcf4 influence their identity and function?

METHODS: We investigated cell specification in small intestinal crypts and colon tumors using conditional Tcf7l2 deletion, cell type-specific Cre recombinases, and reporter alleles in mice. Transcriptomic (single-cell and bulk RNA sequencing) and histological analyses were performed and complemented by microbiome profiling, antibiotic treatment, and intestinal organoids to functionally validate the main findings.

RESULTS: The inactivation of Tcf4 depletes Paneth cells and antimicrobial peptides, disrupting the gut microbiota balance. In secretory progenitors, loss of Tcf4 shifts differentiation toward goblet cells. In the small intestine, alternative secretory progenitors produce Wnt ligands to support stem cells and epithelial renewal in the absence of Paneth cells. In colon tumors, Paneth-like cells form a tumor cell population, express Wnt ligands, and require Tcf4 for their identity. Loss of Tcf4 redirects their differentiation toward goblet cells.

CONCLUSIONS: Tcf4 controls the balance between Paneth and goblet cells and is essential for antimicrobial peptide production in the small intestine. In colon adenomas, Paneth-like tumor cells drive antimicrobial gene expression and provide Wnt3 ligands, which may have implications for cancer therapy.},
}

Animals
*Intestine, Small/metabolism/pathology/microbiology
Mice
*Colonic Neoplasms/pathology/genetics/microbiology/metabolism
Paneth Cells/metabolism
*Transcriptome
*Transcription Factor 4/metabolism/genetics
Humans
Cell Differentiation
*Gastrointestinal Microbiome
Wnt Signaling Pathway
Organoids/metabolism
alpha-Defensins/metabolism
Goblet Cells/metabolism

@article {pmid40221653,
year = {2025},
author = {Babalola, OO and Adebayo, AA and Enagbonma, BJ},
title = {Shotgun metagenomics dataset of the core rhizo-microbiome of monoculture and soybean-precedent carrot.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {26},
pmid = {40221653},
issn = {2730-6844},
mesh = {*Daucus carota/microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Glycine max/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: Carrot is a significant vegetable crop contributing to agricultural diversity and food security, but less is known about the core microbiome associated with its rhizosphere. More so, the effect of preceding crop and cropping history on the composition and diversity of carrot rhizo-microbiome remains largely unknown. With shotgun metagenomics, the study unveils how cropping systems direct rhizo-microbiome structure and functions, previously limited by other methods.

DATA DESCRIPTION: Metagenomic-DNA molecule was extracted from four replicates each (12 samples) of a distant bulk soil and the rhizosphere soils from monoculture and soybean-precedent carrots, with the Power soil® DNA Isolation kit. The DNA samples were subjected to Next Generation Sequencing using the Illumina Novaseq X Plus (PE 150) platform. Raw sequencing reads were assembled and annotated with MEGAHIT and LCA algorithms in MEGAN software respectively, before a quality control check was done with FASTP. CD-Hit was used to de-replicate the sequences and the removal of host genomic-DNA and contaminant sequences was done with Bowtie2. The clean sequence data, in FastQ files, were analyzed for taxonomic classification and functional diversity of the rhizosphere microbiome using the Micro_NR and KEGG database respectively. The findings provide insights into microbiome dynamics, with potential implications for sustainable agricultural practices.},
}

*Daucus carota/microbiology
*Metagenomics/methods
*Rhizosphere
*Glycine max/microbiology/growth & development
*Microbiota
Soil Microbiology
High-Throughput Nucleotide Sequencing

@article {pmid40221592,
year = {2025},
author = {Butler, MI and Kittel-Schneider, S and Wagner-Skacel, J and Mörkl, S and Clarke, G},
title = {The Gut Microbiome in Anxiety Disorders.},
journal = {Current psychiatry reports},
volume = {},
number = {},
pages = {},
pmid = {40221592},
issn = {1535-1645},
abstract = {PURPOSE OF REVIEW: We aim to update readers on the latest evidence regarding the role of the gut microbiome in generalized anxiety disorder (GAD), panic disorder (PD), agoraphobia, and social anxiety disorder (SAD). This review summarises the literature on microbiome composition and function in these conditions, provides insights about causality and mechanisms and evaluates current evidence for microbiome-based interventions in anxiety disorders.

RECENT FINDINGS: Most studies exploring the microbiome in anxiety disorders are small, cross-sectional studies. Nevertheless, some consistent findings emerge. Bacterial taxa such as Eubacterium, Coprococcus and Faecalibacterium may be depleted in GAD. Studies in PD and SAD are scarce and, to our knowledge, there have been no studies conducted in agoraphobia. Probiotics may help reduce anxiety symptoms, although the majority of studies have been in non-clinical cohorts. Large, prospective studies are required to further elucidate the role of the microbiome-gut-brain axis in anxiety disorders. Microbiome-based interventions hold promise, but randomised controlled trials in clinical populations with relevant diagnoses are now warranted and urgently required.},
}

@article {pmid40221450,
year = {2025},
author = {Kim, KS and Noh, J and Kim, BS and Koh, H and Lee, DW},
title = {Refining microbiome diversity analysis by concatenating and integrating dual 16S rRNA amplicon reads.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {57},
pmid = {40221450},
issn = {2055-5008},
support = {RS-2021-NR056579//National Research Foundation of Korea (NRF)/ ; RS-2023-KH141436//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 200118770//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Metagenome ; Colitis, Ulcerative/microbiology ; DNA, Bacterial/genetics ; Republic of Korea ; Phylogeny ; Feces/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the role of human gut microbiota in health and disease requires insights into its taxonomic composition and functional capabilities. This study evaluates whether concatenating paired-end reads enhances data output for gut microbiome analysis compared to the merging approach across various regions of the 16S rRNA gene. We assessed this approach in both mock communities and Korean cohorts with or without ulcerative colitis. Our results indicate that using the direct joining method for the V1-V3 or V6-V8 regions improves taxonomic resolution compared to merging paired-end reads (ME) in post-sequencing data. While predicting microbial function based on 16S rRNA sequencing has inherent limitations, integrating sequencing reads from both the V1-V3 and V6-V8 regions enhanced functional predictions. This was confirmed by whole metagenome sequencing (WMS) of Korean cohorts, where our approach improved taxa detection that was lost using the ME method. Thus, we propose that the integrated dual 16S rRNA sequencing technique serves as a valuable tool for microbiome research by bridging the gap between amplicon sequencing and WMS.},
}

*RNA, Ribosomal, 16S/genetics
Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Metagenome
Colitis, Ulcerative/microbiology
DNA, Bacterial/genetics
Republic of Korea
Phylogeny
Feces/microbiology
Biodiversity
High-Throughput Nucleotide Sequencing

@article {pmid40221415,
year = {2025},
author = {Xu, C and Sun, P and Jiang, Q and Meng, Y and Dong, L and Wang, X and Hu, X and Li, C and Li, G and Zheng, R and You, X and Yang, X},
title = {Tissue-resident Klebsiella quasipneumoniae contributes to progression of idiopathic pulmonary fibrosis by triggering macrophages mitophagy in mice.},
journal = {Cell death discovery},
volume = {11},
number = {1},
pages = {168},
pmid = {40221415},
issn = {2058-7716},
support = {81973383//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204488//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Idiopathic pulmonary fibrosis (IPF) is a progressive and chronic interstitial lung disease with unclear underlying pathogenic mechanisms. Dysbiosis of the lung microbiota is believed to be associated with the development of fibrosis; however, the roles of the microbiome in the respiratory functions of hosts with IPF remain poorly understood. To investigate the relationship between the lung microbiome and the pathological processes of idiopathic pulmonary fibrosis under laboratory conditions, C57BL/6 J mice were exposed to bleomycin and observed at 7, 14, 21, and 28 days post-exposure. 16S rDNA analysis revealed that the lung microbial community exhibited dysbiosis in the bleomycin-induced pulmonary fibrosis model, characterized by an abnormally high proportion of Klebsiella quasipneumoniae (K. quasipneumoniae), as confirmed by RNA fluorescence in situ hybridization. Throughout the progression of experimental pulmonary fibrosis, Tax4Fun analysis indicated that the abundance of K. quasipneumoniae differed significantly between model mice and control mice, correlating with the sustained activation of reactive oxygen species (ROS) pathways. Importantly, the dysbiosis of K. quasipneumoniae may serve as a critical factor triggering increased ROS levels, accompanied by macrophage mitophagy, ultimately leading to the overexpression of TGF-β1, a key player in the pathogenesis of pulmonary fibrosis. These findings suggest that lung microbiota dysbiosis exacerbates the progression of bleomycin-induced pulmonary fibrosis related to macrophage mitophagy.},
}

@article {pmid40221043,
year = {2025},
author = {Badhan, A and Wang, Y and Terry, S and Gruninger, R and Guan, LL and McAllister, TA},
title = {Interplay of rumen microbiome and the cattle host in modulating feed efficiency and methane emissions.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26063},
pmid = {40221043},
issn = {1525-3198},
abstract = {Given that the majority of energy and protein supplied to cattle arises as a result of ruminal fermentation, the rumen microbiome plays a key role in determining host feed efficiency and methane (CH4) emissions. Some reports suggests that a less diverse rumen microbiome is associated with improved feed efficiency, while other studies suggest that microbial diversity does not differ between low- and high-efficiency cattle of the same breed, fed identical diets. While reducing enteric CH4 emissions offers a dual benefit in terms of improved feed efficiency and a reduced environmental footprint; recent findings indicate that these outcomes are not always consistent in ruminants. The composition of the rumen microbiome is mainly determined by diet but is also influenced by host genetics and physiological parameters such as rumen volume, rate of passage and rumination. Reduced microbial diversity may impair the ability of cattle to adapt to frequent changes in diet and the environment. Hydrogen exchange and capture are the energetic foundation of the rumen microbiome, and considerable resources have been invested in developing additives that redirect hydrogen flow toward alternative sinks and away from the reduction of CO2 to CH4. These additives reduce enteric CH4 emissions by 30-80%, yet the anticipated gains in feed efficiency remain inconsistent. Strategies to improve the feed efficiency of cattle production must consider the multifaceted interactions among the host, rumen microbiome, and diet to ensure the sustainable intensification of cattle production while maintaining the social license for milk and meat production.},
}

@article {pmid40221038,
year = {2025},
author = {Flynn, A and Leech, J and McFadden, M and McAloon, C and Paul-Murphy, J and Crispie, F and Cotter, PD and McAloon, C and Kennedy, E},
title = {The effects of offering adequate-quality or high-quality colostrum on the passive immunity, health, growth and fecal microbiome development of dairy heifer calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26165},
pmid = {40221038},
issn = {1525-3198},
abstract = {Colostrum quality is influenced by multiple factors, including its microbial load, which is determined by the cleanliness of collection and storage conditions. Additionally, the dam's diet and immune status play a crucial role in shaping colostrum quality by affecting immunoglobulin (IgG) concentrations. While many factors contribute to colostrum quality, this study will specifically use IgG content as the primary measure of quality. It is well established that feeding low-quality colostrum negatively affects calf health and growth, while feeding good-quality colostrum leads to better outcomes. However, it remains unclear if feeding colostrum above the recommended quality threshold offers additional benefits for calf health and growth. This study compared the effects of adequate versus high-quality colostrum on dairy heifer calf growth, health, and the development of the fecal microbiome during the first 15 weeks of life. We also measured the levels of apparent efficacy of absorption of IgG in both groups. Colostrum quality was initially determined and measured before feeding using a Brix refractometer (only feeding a minimum of 21% Brix); 93 heifer calves were assigned to treatment based on this data. Subsequently, laboratory analyses were conducted using radial immunodiffusion assays to measure the exact IgG levels in the colostrum; 72 calves were selected for continuation in the experiment based on the highest (n = 36) and lowest (n = 36) IgG levels in the colostrum. For these 72 calves, laboratory analyses were conducted using radial immunodiffusion assays to measure the exact IgG levels in the colostrum at the point of feeding and in the calf serum at 24 h post-feeding. To ensure a fair comparison, the groups were balanced for calf birthweight, breed, and dam parity. Serum IgG at 24 h, weight, and health data were analyzed in SAS using linear mixed models and logistic regression. Alpha and β diversity were analyzed using R with ANOVA, PERMANOVA, and Benjamini-Hochberg p-value adjustments. Calves fed colostrum with a high IgG content (123.0 mg/ml IgG) exhibited higher rates of passive transfer compared with those fed adequate-quality colostrum (85.2 mg/ml IgG). Both groups had passive transfer rates > 23 mg/ml IgG. Health outcomes were similar between the 2 groups, and average daily gain during the pre-weaning period was comparable, with calves gaining an average of 0.62 kg per day. Measures of α and β diversity in the fecal microbiome showed similar development in both groups. Apparent absorption efficacy was lower in calves fed high-quality colostrum (24.9%) compared with those fed adequate-quality colostrum (29.3%). The findings of this study support current recommendations for colostrum quality and suggest that calves may have a limited capacity to absorb higher concentrations of IgG. While feeding higher-quality colostrum did not lead to significant improvements in growth, health, or microbiome diversity, it demonstrated that adequate-quality colostrum can be equally effective when combined with best practice management. Further research is needed to better understand the relationships between immunoglobulin absorption efficiency, calf health, microbiome development, and growth performance.},
}

@article {pmid40220988,
year = {2025},
author = {Puel, EM and Taruhn, LF and Damé-Teixeira, N and Stefani, CM and Lataro, RM},
title = {Is there a link between the abundance of nitrate-reducing bacteria and arterial hypertension? A systematic review.},
journal = {Nitric oxide : biology and chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.niox.2025.04.001},
pmid = {40220988},
issn = {1089-8611},
abstract = {CONTEXT: Nitric oxide is a vasodilator molecule that acts on blood pressure (BP) control, and its production can occur through the reduction of nitrates by oral or intestinal nitrate-reducing bacteria. However, the relationship between nitrate-reducing bacteria and arterial hypertension (HTN) remains under debate.

OBJECTIVE: Systematically review if there is an association between the abundance of oral and intestinal nitrate-reducing bacteria and the occurrence of HTN in humans.

MEDLINE, Scopus, Cochrane Library, EMBASE, LILACS, Web of Science, Livivo, ProQuest Dissertations, and Google Scholar were searched for eligible articles until February 10th, 2024. Studies were included if they: (1) were observational studies or clinical trials; (2) included adults (≥ 18 years old) with HTN (systolic BP ≥130 mmHg and/or diastolic BP >80 mmHg and/or use of BP lowering medication); (3) compared (or not) to no-HTN adults; and (4) used next-generation sequencing microbiome analysis to identify bacterial taxa in the oral and/or gut nitrate-reducing bacteria.

RESULTS: The search identified 9365 articles, and 28 were included in the study after applying the inclusion and exclusion criteria; 23 articles assessed the gut microbiota, 4 assessed the oral microbiota, and 1 that assessed both. Depletion of nitrate-reducing bacteria was not consistently showed in the studies. The included studies reported reduction, increase, and no change in the nitrate-reducing bacteria genera or species in oral or gut microbiota.

CONCLUSION: We found no association between the abundance of oral and gut nitrate-reducing bacteria and the occurrence of HTN in humans.

REGISTRATION: PROSPERO identification number CRD42022315891.},
}

@article {pmid40220894,
year = {2025},
author = {Kinnunen, O and Kruglova, A and Jensen, MM and Kuokkanen, A and Smets, BF and Mikola, A},
title = {Shift in activated sludge microbiomes associated with nitrite accumulation and high nitrous oxide emissions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121591},
doi = {10.1016/j.envres.2025.121591},
pmid = {40220894},
issn = {1096-0953},
abstract = {Nitrous oxide (N2O) emissions can constitute over half of the carbon footprint of a wastewater treatment plant (WWTP), and emission peaks frequently correlate with nitrite (NO2[-]) concentrations. However, connections between the microbiome and high N2O and NO2[-] levels are not well-documented. Here, we characterize the microbiomes in several parallel lines of a WWTP during massive N2O emissions (20% of influent nitrogen load) with prolonged NO2[-] accumulation in most lines, aiming to identify key differences between communities in lines with high and low NO2[-] concentrations. The abundance of nitrite-oxidizing bacteria (NOB) was extremely low in the lines with NO2[-] accumulation, which also had slightly lower abundances of ammonia-oxidizing bacteria (AOB). Some incomplete denitrifiers were more abundant in the lines with NO2[-] accumulation. Lines without NO2[-] had a higher relative abundance of filamentous bacteria and better floc formation. These findings confirmed our hypothesis that loss of NOB caused NO2[-] accumulation, inducing increased N2O emissions. AOB are suspected to be the main source of N2O during the studied period, with a likely contribution from heterotrophic denitrifiers. A few species were identified as interesting candidates for further study regarding their potential role in increased N2O emission from WWTPs. Long-term microbiome monitoring is necessary to understand the changes in the microbiome that might initiate NO2[-] accumulation and high N2O emissions.},
}

@article {pmid40220854,
year = {2025},
author = {Olah, P and Reuvers, N and Radai, Z and Varadi, A and van Lierop, A and Wachtmeister, T and Plante, S and Chaskar, P and Thomas, C and Julia, V and Alenius, H and Homey, B},
title = {Microbe-Host Interaction in Rosacea and its Modulation Through Topical Ivermectin.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.03.031},
pmid = {40220854},
issn = {1523-1747},
abstract = {Rosacea is characterized by inflammatory lesions, often accompanied by an increased density of the common skin mite Demodex folliculorum. Although rosacea shows a high prevalence and significantly affects the quality of life of patients, the underlying mechanisms, especially the role of cutaneous dysbiosis are largely unknown. Hence, we aimed to systematically characterize disease severity of rosacea patients in the context of mite density, the cutaneous microbiome and the host's transcriptome before and after 30 days of topical 1% ivermectin cream treatment. At day 30, a marked decrease in mite density was observed in 87.5% of patients. At day 0, distinct microbial community changes included the decrease in Cutibacterium acnes abundance, while Staphylococcus epidermidis colonization increased when compared to healthy volunteers. Interestingly, the insect symbiont Snodgrassella alvi was recovered from a highly Demodex-colonized patient and eradicated by day 30 of treatment. Although topical ivermectin did not affect bacterial dysbiosis, the host's transcriptome significantly normalized and an "ivermectin transcriptomic signature" was defined. Findings of the present study support that rosacea lesions are associated with dysbiosis. However, improvement of clinical signs during topical ivermectin is not associated with normalization of the bacterial microbiome, but rather a decrease of transcriptomic dysregulation and mite density.},
}

@article {pmid40220779,
year = {2025},
author = {Porcari, S and Ianiro, G and , },
title = {Microbiome testing in clinical practice - Authors' reply.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {10},
number = {5},
pages = {414-415},
doi = {10.1016/S2468-1253(25)00063-9},
pmid = {40220779},
issn = {2468-1253},
}

@article {pmid40220778,
year = {2025},
author = {Singh, A and Bhardwaj, A and Midha, V and Sood, A},
title = {Microbiome testing in clinical practice.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {10},
number = {5},
pages = {414},
doi = {10.1016/S2468-1253(24)00432-1},
pmid = {40220778},
issn = {2468-1253},
}

@article {pmid40220558,
year = {2025},
author = {Darriaut, R and Roose-Amsaleg, C and Vanhove, M and Monard, C},
title = {Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems.},
journal = {Microbiological research},
volume = {297},
number = {},
pages = {128178},
doi = {10.1016/j.micres.2025.128178},
pmid = {40220558},
issn = {1618-0623},
abstract = {Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.},
}

@article {pmid40220550,
year = {2025},
author = {Silva, CJFD and Silva, CVFD and Cardoso, AM and de Oliveira Santos, E},
title = {Exploring clinical parameters and salivary microbiome profiles associated with metabolic syndrome in a population of Rio de Janeiro, Brazil.},
journal = {Archives of oral biology},
volume = {175},
number = {},
pages = {106251},
doi = {10.1016/j.archoralbio.2025.106251},
pmid = {40220550},
issn = {1879-1506},
abstract = {OBJECTIVES: This study investigates for the first time the association between metabolic syndrome and oral microbial profiles in a population-based sample from Rio de Janeiro, Brazil.

DESIGN: We assessed 66 volunteers, collecting detailed sociodemographic, anthropometric, and clinical data alongside salivary samples for metagenomic analysis.

RESULTS: Our findings reveal significant differences in anthropometric parameters, including waist circumference, glycemia, High-Density Lipoprotein (HDL), and triglycerides between the metabolic syndrome and control groups. Increased abundance of Bacteroidetes and Bacteroidia was observed in the metabolic syndrome group, suggesting a potential link between these phyla and metabolic dysregulation. While no significant differences in alpha diversity were found between the overall groups, stratification by body mass index (BMI) indicated that the normal weight subgroup without Metabolic Syndrome exhibited notable variations compared to overweight and obese individuals.

CONCLUSIONS: This study identifies specific shifts in oral microbiota composition that are associated with metabolic syndrome, highlighting their potential as microbial biomarkers for this condition. These findings suggest a link between oral dysbiosis and metabolic dysregulation, providing new insights into the pathophysiology of metabolic syndrome. Additionally, the results pave the way for the development of non-invasive diagnostics tools and targeted therapies that leverage the oral microbiome's role in systemic health.},
}

@article {pmid40220427,
year = {2025},
author = {Sun, X and Qin, B and Guo, A and Gui, J and Weng, J and Ye, J and Feng, S and Sang, M},
title = {Withaferin A maintained microbiome and metabolome features in A53T transgenic mice via multi-omics integrated analysis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {141},
number = {},
pages = {156725},
doi = {10.1016/j.phymed.2025.156725},
pmid = {40220427},
issn = {1618-095X},
abstract = {BACKGROUND: Withaferin A (WFA), a naturally occurring compound, has shown promise as a therapeutic agent for Parkinson's disease (PD), a neurodegenerative disorder associated with motor and gastrointestinal dysfunctions. However, its effects on gut microbiota metabolism remain poorly understood.

PURPOSE: This study aimed to elucidate the neuroprotective mechanisms of WFA in a PD mouse model by investigating its regulation of gut microbiota composition, metabolic pathways, and correlations with brain spatial metabolomics.

METHODS: Human SNCA-transgenic (A53T) mice were treated with WFA and evaluated using behavioral tests, immunohistochemistry, Western blot, and ELISA to assess motor/cognitive functions and PD-related pathology. Gut microbiota composition was analyzed via 16S rRNA sequencing, while untargeted fecal metabolomics and brain spatial metabolomics were employed to identify metabolic alterations.

RESULTS: WFA significantly improved motor performance, alleviated cognitive deficits, restored intestinal barrier integrity, and reduced neuroinflammation. It elevated the abundance of anti-inflammatory gut bacteria (e.g., Bifidobacterium, Dubosiella, Akkermansia) and reversed 55 fecal metabolites linked to sphingolipid metabolism, serotonergic synapses, and neuroactive ligand- receptor interactions. Spatial metabolomics revealed WFA's regulation of sphingolipid signaling pathways, including sphingosine kinase (Sphk1), ceramidase, sphingosine 1-phosphate receptor (S1PR5), and endocannabinoid receptor CB2 expression. Correlation analysis indicated a link between brain metabolite content and gut microbiota abundance.

CONCLUSION: Our findings highlight a potential mechanism of WFA that repairs neurons by modulating the sphingolipid signaling pathway within the microbiota-gut-brain axis.},
}

@article {pmid40220252,
year = {2025},
author = {Rezaei, AR and Ates, F and Sulik, A and Toczyłowski, K},
title = {'Smart', microbiome-sparing antibacterial therapy with a focus on the novel Lolamicin: an overview.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40220252},
issn = {1439-0973},
abstract = {PURPOSE: Antibiotic resistance (AR) is an escalating worldwide health emergency, requiring inventive strategies for antibiotic treatment. This review examines the tactics used in designing smart antibiotics, with a specific emphasis on the mechanism of action of lolamicin, a newly developed microbiome-sparing antibiotic.

METHODS: We review the recent advances in smart antibiotic development, particularly those aiming to preserve the gut microbiome while effectively targeting pathogens. The study focuses on lolamicin's selective targeting mechanism, its inhibition of the LolCDE complex in Gram-negative bacteria.

RESULTS: Lolamicin works by blocking the LolCDE complex, which is crucial for transporting lipoproteins in Gramnegative bacteria. It offers a significant improvement compared to conventional antibiotics and other microbiomesparing options by safeguarding the microbiome and reducing the development of resistance. However, its limited range of effectiveness - namely against certain harmful bacteria such as Pseudomonas aeruginosa - and the possibility of bacteria becoming resistant to it, remain areas of concern.

CONCLUSION: Lolamicin presents a hopeful resolution by selectively attacking Gram-negative bacteria while leaving the beneficial gut flora unharmed. Further investigation and rigorous clinical testing are essential to fully harness its promise and confirm its long-term utility in combating antibiotic resistance.},
}

@article {pmid40220199,
year = {2025},
author = {Wasim, R and Sumaiya, and Ahmad, A and Anwar, A and Salman, A},
title = {Microbial imbalance in the gut: a new frontier in Rheumatoid arthritis research.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {40220199},
issn = {1568-5608},
abstract = {A chronic autoimmune illness that causes joint destruction and inflammation, rheumatoid arthritis (RA) often results in disability. Genetic, environmental, and immune system variables all have a role in the pathophysiology of RA. The complex community of bacteria that live in the gastrointestinal system, known as the gut microbiota, has been implicated in the onset and progression of RA in recent years, according to mounting data. An imbalance in the gut microbiota's composition, known as dysbiosis, has been noted in RA patients. This imbalance may impact inflammatory pathways and immunological responses, which in turn may contribute to the development and severity of the illness. Research has shown that some bacterial species, including Firmicutes, Bacteroidetes, and Proteobacteria, are either more abundant or less prevalent in RA patients than in healthy people. The gut-immune system axis may be modulated, immunological tolerance may be affected, and pro-inflammatory cytokine production may be enhanced by these microbial changes, all of which may lead to systemic inflammation linked to RA. Moreover, changes in intestinal permeability and a rise in microbial metabolite translocation may make autoimmune reactions worse. Probiotics, antibiotics, and dietary changes have also been investigated as possible treatment approaches to help RA patients regain the balance of their gut microbiota. Still up for debate, however, are the precise ways in which the gut microbiome affects RA. Comprehending the complex connection between gut microbiota and RA may give new perspectives on managing and preventing the condition, as well as future prospects for medicines that target the microbiome.},
}

@article {pmid40220189,
year = {2025},
author = {Knoppersen, RS and Bose, T and Coutinho, TA and Hammerbacher, A},
title = {Inside the Belly of the Beast: Exploring the Gut Bacterial Diversity of Gonipterus sp. n. 2.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {27},
pmid = {40220189},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Eucalyptus/parasitology/chemistry ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Diet ; South Africa ; *Coleoptera/microbiology/physiology ; Gas Chromatography-Mass Spectrometry ; Introduced Species ; Biodiversity ; },
abstract = {The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC-MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.},
}

Animals
*Gastrointestinal Microbiome
*Eucalyptus/parasitology/chemistry
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Diet
South Africa
*Coleoptera/microbiology/physiology
Gas Chromatography-Mass Spectrometry
Introduced Species
Biodiversity

@article {pmid40220054,
year = {2025},
author = {Brubaker, L and Horsley, H and Khasriya, R and Wolfe, AJ},
title = {Microbiologist in the Clinic: Antibiotic Dependent in her 30 s.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {40220054},
issn = {1433-3023},
abstract = {In this third episode of the Microbiologist in the Clinic series, clinicians and laboratory scientists share their perspectives about a 32 y/o female who has become antibiotic-dependent for her urinary symptoms. Despite escalating methods of antibiotic administration, the patient has persistent and recurrent "UTI" symptoms. Extensive testing has not provided guidance for her treating clinicians. The challenges of this clinical presentation are discussed with evidence for evaluation and treatment.},
}

@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 {pmid40219669,
year = {2025},
author = {Murray, J and Kefayat, A and Finlayson, M and Seenan, JP and Hsu, R and Din, S},
title = {RCPE in association with the American College of Gastroenterology and the Scottish Society of Gastroenterology - Gastroenterology: A global perspective.},
journal = {The journal of the Royal College of Physicians of Edinburgh},
volume = {},
number = {},
pages = {14782715251332318},
doi = {10.1177/14782715251332318},
pmid = {40219669},
issn = {2042-8189},
abstract = {On 6 November 2024, the Royal College of Physicians of Edinburgh (RCPE) hosted its annual gastroenterology symposium, marking the first collaboration with the American College of Gastroenterology (ACG) and the Scottish Society of Gastroenterology (SSG). The event addressed key global challenges in gastroenterology, including obesity, liver disease, inflammatory bowel disease (IBD), the gut microbiome, endoscopy quality and artificial intelligence (AI) applications. Discussions emphasised the growing burden of metabolic dysfunction-associated steatotic liver disease (MASLD), with promising pharmacologic and endoscopic interventions emerging. Advances in microbiome-targeted therapies, including faecal microbiota transplantation (FMT), were explored for recurrent Clostridium difficile infection and IBD. Professor David Rubin delivered the esteemed Sir Stanley Davidson lecture, highlighting the era of disease modification in IBD, emphasising early intervention and personalised treatment strategies. The symposium also addressed the role of AI in improving endoscopic detection rates and optimising resource allocation. This international collaboration underscored the importance of a multidisciplinary approach to tackling global digestive diseases, integrating clinical innovation, policy interventions and technological advancements. The event fostered knowledge exchange among global experts, aiming to advance patient care and improve long-term outcomes in gastroenterology.},
}

@article {pmid40219624,
year = {2025},
author = {Kanbay, M and Ozbek, L and Guldan, M and Abdel-Rahman, SM and Sisman, U and Mallamaci, F and Zoccali, C},
title = {Nutrition, cognition and chronic kidney disease: A comprehensive review of interactions and interventions.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e70045},
doi = {10.1111/eci.70045},
pmid = {40219624},
issn = {1365-2362},
abstract = {BACKGROUND: Cognitive impairment is a prevalent complication in chronic kidney disease (CKD), ranging from mild deficits in early stages to more severe conditions, such as mild cognitive impairment and dementia in advanced stages. CKD patients exhibit reduced performance in memory, attention, language, visuospatial abilities and executive functions.

RESULTS AND DISCUSSION: Contributing factors include uraemic toxins, structural brain changes, blood-brain barrier dysfunction, anaemia and comorbidities like diabetes mellitus. Malnutrition, affecting nearly half of CKD patients, exacerbates cognitive decline through inflammation, oxidative stress and protein-energy wasting. Nutritional deficiencies, particularly in protein, vitamin D, B vitamins, omega-3 fatty acids and antioxidants, are linked to impaired cognition. Emerging evidence highlights the role of the gut-brain axis, with gut-derived uraemic toxins and microbiome alterations contributing to cognitive dysfunction. Processed foods and microplastics further compound risks by promoting inflammation and neurotoxicity. Dialysis and kidney transplantation offer opportunities for cognitive recovery, though challenges remain, particularly in haemodialysis patients. Nutritional interventions, including tailored protein intake, micronutrient supplementation and dietary counselling, are critical for mitigating cognitive decline. Addressing CKD comorbidities, such as anaemia and diabetes through targeted nutritional and pharmacological strategies, improves outcomes. Integrating psychological and social support enhances quality of life, given the high prevalence of anxiety and depression in CKD patients.

CONCLUSIONS: Future research should focus on personalized nutrition, gut microbiota modulation and routine cognitive assessments to optimise care. A holistic approach combining medical, nutritional and psychosocial strategies is essential for improving cognitive and overall health in CKD patients.},
}

@article {pmid40219203,
year = {2025},
author = {Aizaz, M and Lubna, and Hashmi, SS and Khan, MA and Jan, R and Bilal, S and Kim, KM and Al-Harrasi, A and Asaf, S},
title = {Unraveling the Complexities of Flowering in Ornamental Plants: The Interplay of Genetics, Hormonal Networks, and Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071131},
pmid = {40219203},
issn = {2223-7747},
abstract = {In ornamental plants, one of the most complex life processes, i.e., flowering, is regulated by interaction between the microbiota, hormones, and genes. Flowering plays an integral role in overall development and is quintessential for reproduction. Considering its importance, this review explores the complex mechanisms that determine the induction of flowering, highlighting the relationship between hormonal and genetic networks as well as the growing significance of the microbiome. Important genes involved in genetic control include FT, SOC1, and LFY. These genes react to environmental stimuli like photoperiod and vernalization. Auxins, cytokinin, and gibberellins are only a few hormone pathways important for floral growth and timing. The importance of plant-microbe interactions has been emphasized by current research, which shows that the microbiome affects flowering through processes like hormone production and availability of food. A comprehensive understanding of flowering induction is possible by integrating results from microbiota, hormones, and genetics studies, which may improve the breeding and culture of ornamental plants. For researchers to understand the complexity of flowering in ornamental plants and develop unique breeding strategies and improved floral qualities, it is critical to use interdisciplinary approaches, as this comprehensive investigation demonstrates.},
}

@article {pmid40219101,
year = {2025},
author = {Fouad, N and El-Zayat, EM and Amr, D and El-Khishin, DA and Abd-Elhalim, HM and Hafez, A and Radwan, KH and Hamwieh, A and Tadesse, W},
title = {Characterizing Wheat Rhizosphere Bacterial Microbiome Dynamics Under Salinity Stress: Insights from 16S rRNA Metagenomics for Enhancing Stress Tolerance.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/plants14071033},
pmid = {40219101},
issn = {2223-7747},
abstract = {Salinity is one of the most important abiotic stress factors affecting wheat production. Salt in the soil is a major environmental stressor that can affect the bacterial community in the rhizosphere of wheat. The bacteria in the plant's rhizosphere promote growth and stress tolerance, which vary by variety and location. Nevertheless, the soil harbors some of the most diverse microbial communities, while the rhizosphere selectively recruits according to the needs of plants in a complex harmonic regulation. The microbial composition and diversity under normal and saline conditions were assessed by comparing the rhizosphere of wheat with soil using 16S rRNA gene amplicon sequencing, highlighting the number of operational taxonomic units (OTUs). Taxonomic analyzes showed that the bacterial community was predominantly and characteristically composed of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, and Fibrobacteres, representing the usual microbial profile for the rhizosphere of wheat. Idiomarinaceae, Rheinheimera, Halomonas, and Pseudomonas (a strain of Proteobacteria), together with Gracilibacillus (a strain of Firmicutes Bacilli), were recognized as microbial signatures for the rhizosphere microbiome under saline conditions. This was observed even with unchanged soil type and genotype. These patterns occurred despite the same soil type and genotype, with salinity being the only variable. The collective action of these bacterial phyla in the rhizosphere not only improves nutrient availability but also induces systemic resistance in the plants. This synergistic effect improves plant resistance to salt stress and supports the development of salt-tolerant wheat varieties. These microbial signatures could improve our understanding of plant-microbe interactions and support the development of microbiome-based solutions for salt stress.},
}

@article {pmid40219037,
year = {2025},
author = {Theodoridis, X and Papaemmanouil, A and Papageorgiou, N and Savopoulos, C and Chourdakis, M and Triantafyllou, A},
title = {The Association Between Lifestyle Interventions and Trimethylamine N-Oxide: A Systematic-Narrative Hybrid Literature Review.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071280},
pmid = {40219037},
issn = {2072-6643},
mesh = {Humans ; *Methylamines/blood ; *Exercise/physiology ; *Life Style ; Cardiovascular Diseases/prevention & control ; *Diet, Healthy ; Dietary Supplements ; Biomarkers/blood ; Diet ; Diet, Mediterranean ; },
abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut- and food-derived molecule. Elevated TMAO concentrations have been associated with an increased risk of cardiovascular disease (CVD) and all-cause mortality, highlighting its significance as a potential biomarker for adverse health outcomes. Given these associations, it is hypothesized that lifestyle interventions, such as healthy dietary patterns and exercise, could reduce TMAO concentrations. The aim of this systematic-narrative hybrid literature review was to evaluate the relationship between various lifestyle interventions and TMAO.

METHODS: MEDLINE (via PubMed[®]), Scopus[®], and grey literature were searched until July 2024 for eligible clinical trials. Case reports, case series, case studies and observational studies were excluded, as well as studies that investigated food products, nutraceuticals, dietary supplements or have been conducted in the pediatric population.

RESULTS: In total, 27 studies were included in this review. While some dietary interventions, such as plant-based, high-dairy, very low-calorie ketogenic diet or the Mediterranean diet, were associated with lower TMAO concentrations, others-including high-protein and high-fat diets-were linked to an increase in TMAO concentrations. Studies that incorporated a combination of nutrition and exercise-based intervention presented neutral results.

CONCLUSIONS: The relationship between dietary interventions and TMAO concentration remains controversial. While certain interventions show promise in reducing TMAO levels, others yield mixed or contradictory outcomes. Further research, including well-structured RCTs, is needed to investigate the aforementioned associations.},
}

Humans
*Methylamines/blood
*Exercise/physiology
*Life Style
Cardiovascular Diseases/prevention & control
*Diet, Healthy
Dietary Supplements
Biomarkers/blood
Diet
Diet, Mediterranean

@article {pmid40219016,
year = {2025},
author = {Rouskas, K and Guela, M and Pantoura, M and Pagkalos, I and Hassapidou, M and Lalama, E and Pfeiffer, AFH and Decorte, E and Cornelissen, V and Wilson-Barnes, S and Hart, K and Mantovani, E and Dias, SB and Hadjileontiadis, L and Gymnopoulos, LP and Dimitropoulos, K and Argiriou, A},
title = {The Influence of an AI-Driven Personalized Nutrition Program on the Human Gut Microbiome and Its Health Implications.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071260},
pmid = {40219016},
issn = {2072-6643},
support = {817732//European Union/ ; 2024NA119000001//Sus.Agri.Food National program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Adult ; Female ; Male ; Feces/microbiology ; *Artificial Intelligence ; *Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Diet ; },
abstract = {Background/Objectives: Personalized nutrition programs enhanced with artificial intelligence (AI)-based tools hold promising potential for the development of healthy and sustainable diets and for disease prevention. This study aimed to explore the impact of an AI-based personalized nutrition program on the gut microbiome of healthy individuals. Methods: An intervention using an AI-based mobile application for personalized nutrition was applied for six weeks. Fecal and blood samples from 29 healthy participants (females 52%, mean age 35 years) were collected at baseline and at six weeks. Gut microbiome through 16s ribosomal RNA (rRNA) amplicon sequencing, anthropometric and biochemical data were analyzed at both timepoints. Dietary assessment was performed using food frequency questionnaires. Results: A significant increase in richness (Chao1, 220.4 ± 58.5 vs. 241.5 ± 60.2, p = 0.024) and diversity (Faith's phylogenetic diversity, 15.5 ± 3.3 vs. 17.3 ± 2.8, p = 0.0001) was found from pre- to post-intervention. Following the intervention, the relative abundance of genera associated with the reduction in cholesterol and heart disease risk (e.g., Eubacterium coprostanoligenes group and Oscillobacter) was significantly increased, while the abundance of inflammation-associated genera (e.g., Eubacterium ruminantium group and Gastranaerophilales) was decreased. Alterations in the abundance of several butyrate-producing genera were also found (e.g., increase in Faecalibacterium, decrease in Bifidobacterium). Further, a decrease in carbohydrate (272.2 ± 97.7 vs. 222.9 ± 80.5, p = 0.003) and protein (113.6 ± 38.8 vs. 98.6 ± 32.4, p = 0.011) intake, as well as a reduction in waist circumference (78.4 ± 12.1 vs. 77.2 ± 11.2, p = 0.023), was also seen. Changes in the abundance of Oscillospiraceae_UCG_002 and Lachnospiraceae_UCG_004 were positively associated with changes in olive oil intake (Rho = 0.57, p = 0.001) and levels of triglycerides (Rho = 0.56, p = 0.001). Conclusions: This study highlights the potential for an AI-based personalized nutrition program to influence the gut microbiome. More research is now needed to establish the use of gut microbiome-informed strategies for personalized nutrition.},
}

Humans
*Gastrointestinal Microbiome/physiology
Adult
Female
Male
Feces/microbiology
*Artificial Intelligence
*Precision Medicine/methods
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics
Diet

@article {pmid40219015,
year = {2025},
author = {Lee, NK and Lee, Y and Shin, DS and Choi, YM and Lee, J and Park, E and Paik, HD},
title = {Effect of Lactiplantibacillus plantarum DSW3805 Isolated from Kimchi for Gut Health Attenuating Colonic Inflammation in a Dextran Sulfate Sodium-Induced Mouse Model.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071259},
pmid = {40219015},
issn = {2072-6643},
mesh = {Animals ; Dextran Sulfate ; *Probiotics/pharmacology ; *Colitis/chemically induced/microbiology/therapy ; Mice ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Fermented Foods/microbiology ; Colon/pathology/microbiology/metabolism ; *Lactobacillus plantarum/isolation & purification ; Male ; Fatty Acids, Volatile/metabolism ; Cytokines/metabolism ; Inflammation ; Lactobacillaceae ; Mice, Inbred C57BL ; },
abstract = {Background/Objectives:Lactiplantibacillus plantarum DSW3805 was isolated from Korean kimchi samples to examine its effect in a dextran sulfate sodium (DSS)-induced mouse model. Methods: To induce colitis, mice were treated with DSS for one week before sacrifice (n = 8 per group, total n = 40). Lacticaseibacillus rhamnosus GG (10[9] CFU/day) or probiotics (L. plantarum DSW3805; 10[8] or 10[9] CFU/day) were administered for two weeks. To assess colitis damage, we evaluated the disease activity index, colon tissue, inflammatory factors, the microbiome, short-chain fatty acids, and intestine-related factors. Results: DSS induced colonic tissue damage (colon length, mucus thickness, and colonic crypts), and L. plantarum DSW3805 alleviated the tissue damage. Induced inflammation was reduced by inhibiting TNF-α, IFN-γ, IL-1β, IL-6, IgA, IgG, LTB4, PGE2, and NF-κB protein expression. The ratio of Firmicutes to Bacteroidetes in the PC group (DSS-treated control) was lower than that in the NC (DSS-nontreated control); L. plantarum DSW3805 increased the ratio. Higher concentrations of acetic, propionic, and butyric acids were detected in probiotic groups. In addition, harmful factors, such as calprotectin and β-glucuronidase, were reduced in the probiotic groups. Conclusions:L. plantarum DSW3805 alleviates gut damage by colitis; therefore, it can be used as a functional food to improve gut health.},
}

Animals
Dextran Sulfate
*Probiotics/pharmacology
*Colitis/chemically induced/microbiology/therapy
Mice
Disease Models, Animal
Gastrointestinal Microbiome
*Fermented Foods/microbiology
Colon/pathology/microbiology/metabolism
*Lactobacillus plantarum/isolation & purification
Male
Fatty Acids, Volatile/metabolism
Cytokines/metabolism
Inflammation
Lactobacillaceae
Mice, Inbred C57BL

@article {pmid40219004,
year = {2025},
author = {Cedillo-Flores, R and Cuevas-Budhart, MA and Cavero-Redondo, I and Kappes, M and Ávila-Díaz, M and Paniagua, R},
title = {Impact of Gut Microbiome Modulation on Uremic Toxin Reduction in Chronic Kidney Disease: A Systematic Review and Network Meta-Analysis.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071247},
pmid = {40219004},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Renal Insufficiency, Chronic/microbiology/therapy ; *Uremic Toxins/metabolism/blood ; Synbiotics/administration & dosage ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; Network Meta-Analysis as Topic ; Dysbiosis ; Randomized Controlled Trials as Topic ; Male ; Female ; Cresols/blood ; },
abstract = {Background/Objectives: Chronic kidney disease is associated with increased intestinal barrier permeability, leading to heightened inflammation and oxidative stress. These changes contribute to complications such as cardiovascular disease, anemia, altered mineral metabolism, and CKD progression. Interventions using prebiotics, probiotics, and synbiotics may mitigate dysbiosis and improve intestinal barrier function, Under this premise, the objective of this network meta-analysis was to evaluate the effect of probiotics, prebiotics, and synbiotics in reducing uremic toxins produced by the gut microbiota in CKD patients. Methods: A systematic review and network meta-analysis of randomized clinical trials (RCTs) was performed in the following databases: Web of Science, Scopus, the Cochrane Register of Controlled Trials, and PubMed published between 2019 and 2023. The analysis focused on the use of prebiotics, probiotics, and synbiotics in CKD patients at stages 3 to 5, as per KDIGO guidelines, and their association with reductions in uremic toxins such as Indoxyl Sulfate, p-Cresyl Sulfate, urea, and creatinine. The risk of bias was assessed using the Cochrane risk of bias tool (RoB 2), with evaluations conducted independently by two reviewers, and a third consulted for disagreements. The study follows the PRISMA statement. Results: The studies included 331 patients, primarily male, across CKD stages 3a to 5. The interventions positively impacted the gut microbiota composition, leading to reductions in free and total p-Cresyl Sulfate (SUCRA: 72.6% and 66.2, respectively) and indoxyl sulfate (SUCRA: 88.5% and 83.1%). Conclusions: The findings suggest that modulating the gut microbiota through these interventions can effectively reduce specific uremic toxins. However, further trials are necessary to better understand microbiota modulation and its impact on intestinal bacterial composition (PROSPERO number: CRD42023438901).},
}

Humans
*Gastrointestinal Microbiome/physiology
*Renal Insufficiency, Chronic/microbiology/therapy
*Uremic Toxins/metabolism/blood
Synbiotics/administration & dosage
Prebiotics/administration & dosage
Probiotics/administration & dosage
Network Meta-Analysis as Topic
Dysbiosis
Randomized Controlled Trials as Topic
Male
Female
Cresols/blood

@article {pmid40218992,
year = {2025},
author = {Vanderpeet, CL and Dorey, ES and Neal, ES and Mullins, T and McIntyre, DH and Callaway, LK and Barrett, HL and Dekker Nitert, M and Cuffe, JSM},
title = {Dietary Fibre Modulates Gut Microbiota in Late Pregnancy Without Altering SCFA Levels, and Propionate Treatement Has No Effect on Placental Explant Function.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071234},
pmid = {40218992},
issn = {2072-6643},
support = {APP1028575//National Health and Medical Research Council/ ; },
mesh = {Humans ; Female ; *Dietary Fiber/administration & dosage/pharmacology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Propionates/pharmacology ; *Fatty Acids, Volatile/blood/metabolism ; *Placenta/drug effects/physiology/metabolism ; Adult ; Feces/microbiology ; Butyrates/blood ; Bacteria ; },
abstract = {Background/Objectives: Dietary fibre promotes health, partly by mediating gut microbiota and short-chain fatty acid (SCFA) production. Pregnancy alters the relationship between dietary composition and the gut microbiota, and it is unclear if fibre intake during late pregnancy alters the abundance of SCFA bacteria and circulating SFCA concentrations. The aim of this study was to determine the impact of dietary fibre on faecal microbiome composition and circulating concentrations of SCFA acetate, butyrate, and propionate in late pregnancy. We also aimed to assess the impact of propionate treatment on placental function using cultured placental explants. Methods: 16S rRNA gene amplicon sequencing was performed on faecal DNA collected at 28 weeks of gestation from participants enrolled in the SPRING cohort study consuming a low or adequate fibre diet. Circualting SCFA were assessed. Placental explants were treated with sodium propionate. Results: Fibre intake did not impact microbial diversity or richness but did impact the abundance of specific bacterial genera. Pregnant participants with low-fibre diets had a greater abundance of Bacteroides and Sutterella, and dietary fibre intake (mg/day) negatively correlated with genera, including Sutterella, Bilophila, and Bacteroides. SCFA concentrations did not differ between groups but circulating concentrations of acetate, propionate, and butyrate did correlate with the abundance of key bacterial genera. Propionate treatment of placental explants did not alter mRNA expression of fatty acid receptors, antioxidants, or markers of apoptosis, nor did it impact pAMPK levels. Conclusions: This study demonstrates that the impact of dietary fibre on SCFA concentrations in pregnant women is modest, although this relationship may be difficult to discern given that other dietary factors differed between groups. Furthermore, this study demonstrates that propionate does not impact key pathways in placental tissue, suggesting that previous associations between this SCFA and placental dysfunction may be due to other maternal factors.},
}

Humans
Female
*Dietary Fiber/administration & dosage/pharmacology
Pregnancy
*Gastrointestinal Microbiome/drug effects
*Propionates/pharmacology
*Fatty Acids, Volatile/blood/metabolism
*Placenta/drug effects/physiology/metabolism
Adult
Feces/microbiology
Butyrates/blood
Bacteria

@article {pmid40218980,
year = {2025},
author = {Slöcker-Barrio, M and López-Herce Cid, J and Solana-García, MJ},
title = {The Interplay Between Nutrition and Microbiota and the Role of Probiotics and Symbiotics in Pediatric Infectious Diseases.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071222},
pmid = {40218980},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Child ; *Communicable Diseases/microbiology/therapy/immunology ; Prebiotics/administration & dosage ; *Gastrointestinal Microbiome ; Dietary Supplements ; *Nutritional Status ; *Child Nutritional Physiological Phenomena ; Immunocompromised Host ; },
abstract = {The interplay between nutrition and infectious diseases has been a central theme in health sciences for the last decades due to its great impact on the pediatric population, especially in immunocompromised patients and critically ill children. As conventional treatment and the development of antimicrobials for most infections standard treatment is either limited or not possible, alternative treatment options should be explored. Recent research shows that early enteral nutrition and nutritional supplements (such as probiotics and symbiotics) could have a pivotal role in promoting a healthy microbiome and subsequently preventing and improving outcomes for certain pediatric infectious diseases. However, understanding the specific mechanism of action and tailoring nutritional interventions remains a significant challenge. The optimal dose range for different probiotic strains and prebiotics and the most effective combination for each treatment indication needs further investigation and is yet to be defined. Additionally, in the era of personalized medicine, goal- and patient-directed treatment are key to optimizing and improving outcomes and minimizing potential complications and side effects, especially in complex and immunocompromised patients. The main objectives of this narrative review are 1. to explore the relationship and the complex interactions between microbiota and the human immune system; 2. to describe the influence of nutrition on infectious diseases; 3. to evaluate the impact of supplementation with probiotics and symbiotics in the prevention and treatment of the most relevant infections in children; and 4. to identify knowledge gaps and potential research priorities regarding the use of these supplements in pediatric patients.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Child
*Communicable Diseases/microbiology/therapy/immunology
Prebiotics/administration & dosage
*Gastrointestinal Microbiome
Dietary Supplements
*Nutritional Status
*Child Nutritional Physiological Phenomena
Immunocompromised Host

@article {pmid40218978,
year = {2025},
author = {Zwierz, M and Suprunowicz, M and Mrozek, K and Pietruszkiewicz, J and Oracz, AJ and Konarzewska, B and Waszkiewicz, N},
title = {Vitamin B12 and Autism Spectrum Disorder: A Review of Current Evidence.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071220},
pmid = {40218978},
issn = {2072-6643},
support = {B.SUB.25.437//Medical University of Białystok/ ; },
mesh = {Humans ; *Vitamin B 12/blood/administration & dosage ; *Autism Spectrum Disorder/etiology/blood ; Pregnancy ; Female ; *Vitamin B 12 Deficiency/complications/blood ; Gastrointestinal Microbiome ; Maternal Nutritional Physiological Phenomena ; Dysbiosis ; Brain ; Infant ; },
abstract = {Vitamin B12 (cobalamin) plays a crucial role in neurodevelopment, particularly during pregnancy and early childhood. It is essential for DNA synthesis, red blood cell formation, and nervous system function. Maternal B12 levels are particularly important, as they influence fetal brain development. Inadequate maternal intake during pregnancy may lead to altered neurodevelopmental trajectories and increase the risk of ASD. Postnatally, insufficient dietary cobalamin in infants and young children could further contribute to cognitive and behavioral impairments. One potential mechanism linking low B12 levels to ASD involves its role in the gut microbiota balance. Dysbiosis, commonly observed in individuals with ASD, is associated with increased gut permeability, low-grade inflammation, and disruptions in the gut-brain axis, all of which may contribute to ASD symptoms. Additionally, B12 is essential for neurotransmitter metabolism, particularly in the synthesis of serotonin and dopamine, which regulate mood, cognition, and behavior. Cobalamin also plays a key role in neuronal myelination, which ensures efficient signal transmission in the nervous system. Disruptions in these processes could underlie some of the cognitive and behavioral features associated with ASD. Despite growing evidence, the link between B12 and ASD remains inconclusive due to inconsistent findings across studies. Research suggests that B12 levels may serve as a potential biomarker for disease progression and treatment response. However, many studies rely on single-time-point measurements, failing to account for individual variability, genetic predispositions, dietary intake, and environmental factors, all of which can influence B12 levels and ASD risk. Further longitudinal studies are needed to clarify this relationship.},
}

Humans
*Vitamin B 12/blood/administration & dosage
*Autism Spectrum Disorder/etiology/blood
Pregnancy
Female
*Vitamin B 12 Deficiency/complications/blood
Gastrointestinal Microbiome
Maternal Nutritional Physiological Phenomena
Dysbiosis
Brain
Infant

@article {pmid40218973,
year = {2025},
author = {Lutz, M and Arancibia, M and Moran-Kneer, J and Manterola, M},
title = {Ultraprocessed Foods and Neuropsychiatric Outcomes: Putative Mechanisms.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071215},
pmid = {40218973},
issn = {2072-6643},
support = {CIDI 003/2025//C-ESTRES (Center for Translational Studies in Stress and Mental Health), Universidad de Valpa-raíso, Chile/ ; },
mesh = {Humans ; Gastrointestinal Microbiome ; *Food Handling ; *Mental Disorders/etiology ; *Fast Foods/adverse effects ; Oxidative Stress ; *Diet/adverse effects ; },
abstract = {A body of evidence indicates an association between ultraprocessed foods (UPFs) and health outcomes. Most of it has been obtained through preclinical studies, although a number of observational studies substantiate how a high intake of these products increases the risk of neuropsychiatric disorders, and an increasing amount of dietary intervention studies confirm these findings. The aim of this narrative review is to describe some of the putative mechanisms involved in the deleterious effects of a high intake of UPFs on neuropsychiatric outcomes. A myriad of unhealthy actions may be associated with the consumption of UPFs, and some mechanisms are being discussed. They include UPFs' high caloric density; their high sugar, sodium, and additives content and low amounts of fiber; and a high palatability that induces overconsumption, acting as obesogens. Moreover, thermal treatment of these foods generates oxidative products such as glycotoxins, lipotoxins, and acrolein, all of which affect the brain. The chemical products act, directly or indirectly, on the gut microbiome and affect the gut-brain axis, causing neuroinflammation, oxidative stress, and neurodegeneration. UPFs also exert various epigenetic effects that affect mental health and might explain the intergenerational inheritance of neuropsychiatric disorders. A diet containing a high proportion of these foods has a low nutritional density, including bioactive protective agents such as antioxidant and anti-inflammatory compounds that promote eubiosis. The evidence shows that UPFs intake affects neuropsychiatric outcomes such as neurodegeneration, cognitive decline, dementia, and mood disorders and reinforces the need to promote a healthy dietary pattern throughout all life stages, thus interfering with the current commercial determinants of health.},
}

Humans
Gastrointestinal Microbiome
*Food Handling
*Mental Disorders/etiology
*Fast Foods/adverse effects
Oxidative Stress
*Diet/adverse effects

@article {pmid40218958,
year = {2025},
author = {Porter Starr, KN and Connelly, MA and Wallis, J and North, R and Zhang, Q and Song, K and González-Delgado, JM and Brochu, HN and Icenhour, CR and Iyer, LK and Miller, MG and Huffman, KM and Kraus, WE and Bales, CW},
title = {Effects of Blueberry Consumption on Fecal Microbiome Composition and Circulating Metabolites, Lipids, and Lipoproteins in a Randomized Controlled Trial of Older Adults with Overweight or Obesity: The BEACTIVE Trial.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071200},
pmid = {40218958},
issn = {2072-6643},
support = {N/A//U.S. Highbush Blueberry Council grant/ ; },
mesh = {Humans ; *Blueberry Plants ; *Feces/microbiology ; Male ; Female ; Aged ; *Obesity/microbiology/blood/diet therapy ; Middle Aged ; *Overweight/microbiology/blood/diet therapy ; *Gastrointestinal Microbiome ; *Lipids/blood ; *Lipoproteins/blood ; Biomarkers/blood ; Diet ; },
abstract = {Background/Objectives: Generous consumption of phytonutrient-rich foods, including blueberries, provides benefits to multiple physiologic and metabolic systems. This study explored the potential that regular, generous blueberry intake could favorably modulate fecal microbiome composition in sedentary older (>60 years) men and women with overweight or obesity (BMI ≥ 25 to 32 kg/m[2]). Methods: Participants (n = 55) were randomized to daily consumption of either lyophilized blueberry powder (equivalent to 1.5 cups of blueberries) or an indistinguishable placebo powder; both groups participated in weekly supervised exercise classes. Fecal samples were collected at 0 and 12 weeks and frozen. Following this, 16S rRNA gene sequencing was used to profile each participant's fecal microbiome. Blood biomarkers of cardiometabolic health were measured via nuclear magnetic resonance spectroscopy (NMR) pre- and post-treatment. Results: Comparing the baseline and endpoint results for the blueberry (n = 15) and placebo (n = 19) groups, there were no significant overall compositional differences or differences in the level of diversity in the fecal microbiome. However, in subjects whose diet included blueberry powder, there was a significant enrichment (p = 0.049) in the relative abundance of Coriobacteriales incertae sedis, a taxonomic group of bacteria that facilitates the metabolism of dietary polyphenols. The placebo group exhibited significant reductions in total cholesterol, LDL-C, non-HDL-C, total LDL-P, large LDL-P, and ApoB, while the blueberry group exhibited significant reductions in total HDL-P and ApoA-I after 12 weeks compared to baseline. Conclusions: Generous blueberry consumption may upregulate the ability of the older human gut to utilize dietary polyphenols by altering the fecal microbiome. Longer, larger-scale studies with blueberries or blueberry powder are needed to observe improvements in cardiometabolic risk factors in older adults with overweight or obesity.},
}

Humans
*Blueberry Plants
*Feces/microbiology
Male
Female
Aged
*Obesity/microbiology/blood/diet therapy
Middle Aged
*Overweight/microbiology/blood/diet therapy
*Gastrointestinal Microbiome
*Lipids/blood
*Lipoproteins/blood
Biomarkers/blood
Diet

@article {pmid40218949,
year = {2025},
author = {Lee, SB and Yoo, B and Baeg, C and Yun, J and Ryu, DW and Kim, G and Kim, S and Shin, H and Lee, JH},
title = {A 12-Week, Randomized, Double-Blind, Placebo-Controlled Study to Evaluate the Efficacy and Safety of Lactobacillus plantarum LMT1-48 on Body Fat Loss.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071191},
pmid = {40218949},
issn = {2072-6643},
mesh = {Humans ; *Lactobacillus plantarum ; *Probiotics/administration & dosage/adverse effects/therapeutic use ; Double-Blind Method ; Male ; Female ; *Obesity/therapy/microbiology ; Middle Aged ; Adult ; Gastrointestinal Microbiome ; *Adipose Tissue ; Feces/microbiology ; Body Mass Index ; Treatment Outcome ; Body Composition ; Absorptiometry, Photon ; },
abstract = {OBJECTIVES: This study aims to evaluate the efficacy and safety of probiotics for body fat reduction in obese individuals.

METHODS: A total of 106 participants with a body mass index between 25 and 30 kg/m[2] were randomly assigned to either the experimental group treating with Lactobacillus plantarum LMT1-48 or the placebo group in the placebo-controlled clinical trial. Body composition was assessed by dual-energy X-ray absorptiometry and computed tomography. Fecal samples between the groups were contrasted via DNA sequencing for evaluation of the microbiota and its diversity.

RESULTS: After 12 weeks of follow-up period, the body fat mass decreased significantly, from 30.0 ± 4.4 to 28.3 ± 4.1 kg in the experimental group (p = 0.009). The percentage of body fat in the two groups showed a similar trend (p = 0.004).

CONCLUSIONS: LMT1-48 also positively influenced the microbial taxa linked to obesity analyzed by gut microbiome sequencing. LMT1-48 is a safe and collaborative agent to reduce obesity.},
}

Humans
*Lactobacillus plantarum
*Probiotics/administration & dosage/adverse effects/therapeutic use
Double-Blind Method
Male
Female
*Obesity/therapy/microbiology
Middle Aged
Adult
Gastrointestinal Microbiome
*Adipose Tissue
Feces/microbiology
Body Mass Index
Treatment Outcome
Body Composition
Absorptiometry, Photon

@article {pmid40218922,
year = {2025},
author = {Chatsirisakul, O and Leenabanchong, N and Siripaopradit, Y and Chang, CW and Buhngamongkol, P and Pongpirul, K},
title = {Strain-Specific Therapeutic Potential of Lactiplantibacillus plantarum: A Systematic Scoping Review.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071165},
pmid = {40218922},
issn = {2072-6643},
support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; N/A//Second Century Fund (C2F)/ ; },
mesh = {Humans ; *Probiotics/therapeutic use ; *Lactobacillus plantarum/classification/physiology ; Female ; Oral Health ; Dermatitis, Atopic/therapy ; Dental Caries/therapy ; Species Specificity ; },
abstract = {Objectives: This systematically scoping review aims to evaluate the therapeutic potential and clinical benefits of specific Lactiplantibacillus plantarum (L. plantarum) strains in human health, identifying their strain-specific effects across various medical conditions. Methods: Following the PRISMA for Scoping Reviews (PRISMA-ScR) guidelines and employing the PICO framework, a comprehensive literature search was conducted in the PubMed and Embase databases to identify relevant studies published up to December 2023. Inclusion criteria were rigorously applied to ensure the selection of high-quality studies focusing on the clinical application of distinct L. plantarum stains. Results: This review analyzed several unique strains of L. plantarum across 69 studies, identifying several therapeutic benefits. L. plantarum 299v effectively improved gastrointestinal symptoms, enhanced oral health, and reduced systemic inflammation. L. plantarum IS-10506 exhibited notable immunomodulatory effects, especially in managing atopic dermatitis. L. plantarum LB931 showed promise in decreasing pathogenic colonization, supporting women's vaginal health. Additionally, L. plantarum CCFM8724 demonstrated potential in reducing early childhood caries, highlighting its promise in pediatric oral care. Conclusions: The therapeutic potential of L. plantarum is extensive, with certain strains exhibiting promising clinical benefits for specific health concerns. The findings of this review advocate for the integration of L. plantarum strains into clinical practice, emphasizing the need for further research to elucidate their mechanisms of action, optimal dosages, and long-term safety profiles.},
}

Humans
*Probiotics/therapeutic use
*Lactobacillus plantarum/classification/physiology
Female
Oral Health
Dermatitis, Atopic/therapy
Dental Caries/therapy
Species Specificity

@article {pmid40218905,
year = {2025},
author = {Minaya, DM and Hoss, A and Bhagat, A and Guo, TL and Czaja, K},
title = {Sex-Specific Effect of a High-Energy Diet on Body Composition, Gut Microbiota, and Inflammatory Markers in Rats.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071147},
pmid = {40218905},
issn = {2072-6643},
support = {1R01DC013904/GF/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Rats, Sprague-Dawley ; *Body Composition ; Rats ; *Obesity/etiology/microbiology ; Feces/chemistry/microbiology ; Biomarkers/blood ; *Inflammation ; Sex Factors ; Weight Gain ; Cytokines/blood ; *Energy Intake ; *Diet ; },
abstract = {Background/Objectives: A high-energy-density (HED) diet promotes body weight gain, fat accumulation, and gut dysbiosis, contributing to obesity. The aim of this study was to characterize the initial response to HED diet consumption, as well as identify any sex differences in body composition, systemic inflammation, gut microbiome, and fecal fat excretion in rats. Methods: Male and female Sprague-Dawley rats were fed a low-energy-density (LED) diet for 10 days and were then switched to an HED diet for four weeks. Food intake, body weight, and body composition were measured routinely. Serum samples were collected to measure inflammatory cytokines/chemokines. Fecal samples were collected for microbiome analysis and lipid content. Results: After the HED diet, all rats gained body weight and fat mass, with males exhibiting increased susceptibility to weight gain. Males displayed either a diet-induced obesity phenotype (DIO-P) or a diet-resistant (DR) phenotype, as characterized by their differential body weight gain. Males showed elevated TGF-β levels, while females exhibited increases in Interferon gamma-inducible protein 10 (IP-10), regulated on activation, normal T cell expressed and secreted (RANTES) protein, and basic fibroblast growth factor (FGFb). Changes in gut microbiota composition revealed a reduction in beneficial species, like Bacteroides uniformis and Parabacteroides distasonis, and an increase in species such as Akkermansia muciniphila. Sex differences in fat metabolism were shown in the greater fecal fat excretion observed in males. Conclusions: Our study demonstrates that short-term consumption of a high-energy diet elicits notable sex-specific differences in body weight, body composition, inflammatory markers, gut microbiota, and fat excretion in Sprague-Dawley rats. While we recognize that this study has a small sample size and a short-term intervention, our findings highlight the critical role of sex as a biological variable in diet-induced obesity research.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
Rats, Sprague-Dawley
*Body Composition
Rats
*Obesity/etiology/microbiology
Feces/chemistry/microbiology
Biomarkers/blood
*Inflammation
Sex Factors
Weight Gain
Cytokines/blood
*Energy Intake
*Diet

@article {pmid40218904,
year = {2025},
author = {Jayasinghe, T and Jenkins, J and Medara, N and Choowong, P and Dharmarathne, G and Kong, F and Cho, H and Kim, SH and Zhang, Y and Franco-Duarte, R and Eberhard, J and Spahr, A},
title = {Dietary Fibre Modulates Body Composition, Blood Glucose, Inflammation, Microbiome, and Metabolome in a Murine Model of Periodontitis.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071146},
pmid = {40218904},
issn = {2072-6643},
support = {Philanthropic funding received for the Chair of Oral Lifespan, School of Dentistry, The University of Sydney.//Philanthropic funding received for the Chair of Oral Lifespan, School of Dentistry, The University of Sydney./ ; },
mesh = {Animals ; *Dietary Fiber/administration & dosage/pharmacology ; Male ; *Periodontitis/microbiology/metabolism/diet therapy/blood ; *Metabolome/drug effects ; Mice, Inbred C57BL ; *Blood Glucose/metabolism ; Mice ; *Body Composition/drug effects ; Disease Models, Animal ; *Inflammation ; *Microbiota ; Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {Background: Dietary fibre plays a crucial role in metabolic regulation, inflammation, and microbiome composition. However, its impact on systemic and oral health, particularly in periodontitis, remains unclear. This study investigated the effects of high- and low-fibre diets on body composition, glycaemic control, inflammation, microbiome, and metabolome in a murine model of experimental periodontitis. Methods: Thirty-six male C57BL/6 mice were randomised to a high-fibre (40% fibre) or low-fibre (5% fibre) diet for eight weeks. Body weight, fat mass, lean mass, fasting blood glucose, serum inflammatory markers, alveolar bone loss, and root length were assessed. Oral and faecal microbiome composition was analysed using 16S rRNA sequencing. Metabolomic and short-chain fatty acid (SCFA) profiling was conducted using liquid chromatography-mass spectrometry (LC-MS). Results: Mice on the high-fibre diet exhibited significantly lower body weight (p < 0.0001), fat mass (p = 0.0007), and lean mass (p < 0.0001) compared to the low-fibre group. Fasting blood glucose levels were significantly lower in the high-fibre group (p = 0.0013). TNF-α and IFN-γ levels were significantly elevated in the low-fibre group (p < 0.0001), suggesting a heightened pro-inflammatory state. While alveolar bone loss and root length did not differ significantly, microbiome analysis revealed distinct bacterial compositions (PERMANOVA, p < 0.05), with fibre-fermenting taxa enriched in high-fibre-fed mice. Metabolomic analysis identified 19 significantly altered metabolites, indicating dietary adaptations. Conclusions: A high-fibre diet improves glycaemic control, reduces systemic inflammation, and alters microbial and metabolic profiles in experimental periodontitis. These findings highlight dietary fibre's role in modulating metabolic and inflammatory pathways relevant to periodontal and systemic diseases.},
}

Animals
*Dietary Fiber/administration & dosage/pharmacology
Male
*Periodontitis/microbiology/metabolism/diet therapy/blood
*Metabolome/drug effects
Mice, Inbred C57BL
*Blood Glucose/metabolism
Mice
*Body Composition/drug effects
Disease Models, Animal
*Inflammation
*Microbiota
Gastrointestinal Microbiome
Feces/microbiology

@article {pmid40218900,
year = {2025},
author = {Al-Refai, W and Keenan, S and Camera, DM and Cooke, MB},
title = {The Influence of Vegan, Vegetarian, and Omnivorous Diets on Protein Metabolism: A Role for the Gut-Muscle Axis?.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071142},
pmid = {40218900},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Muscle, Skeletal/metabolism ; *Diet, Vegan ; *Diet, Vegetarian ; *Diet ; *Dietary Proteins/metabolism ; Vegans ; },
abstract = {There has been a growing interest globally in vegan and vegetarian diets over the last decade for a combination of health, ethical, environmental, spiritual, and social reasons. In line with this popularity, research examining the role of plant-based food sources, including vegan and vegetarian diets, in supporting skeletal muscle remodeling and anabolism in humans has also received considerable attention. The emergence of the microbiota-gut-muscle axis, a bidirectional pathway where the gut microbiota impacts skeletal muscle and vice versa, has been suggested as a potential mediator of food and nutrition's influence on the mechanistic processes that regulate muscle mass and function. Considering inherent nutritional differences between vegan, vegetarian, and omnivorous diets related to the fiber and macronutrient content, presence of anti-nutritional factors, and diverse food and supplemental sources for obtaining protein, it stands to reason that the regulation of the microbiota-gut-muscle axis via diet-induced changes in gut microbiota composition and function may be dissimilar. However, whether this translates into differential effects on the skeletal muscle is unclear. This review article aims to provide a contemporary perspective for how variations in gut microbiota linked to vegan, vegetarian, and omnivorous diets may be a potential mechanism for influencing protein metabolism in skeletal muscle mass via a purported microbiota-gut-muscle axis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Muscle, Skeletal/metabolism
*Diet, Vegan
*Diet, Vegetarian
*Diet
*Dietary Proteins/metabolism
Vegans

@article {pmid40218866,
year = {2025},
author = {Altendorfer, B and Benedetti, A and Mrowetz, H and Bernegger, S and Bretl, A and Preishuber-Pflügl, J and Bessa de Sousa, DM and Ladek, AM and Koller, A and Le Faouder, P and Bertrand-Michel, J and Trost, A and Aigner, L},
title = {Omega-3 EPA Supplementation Shapes the Gut Microbiota Composition and Reduces Major Histocompatibility Complex Class II in Aged Wild-Type and APP/PS1 Alzheimer's Mice: A Pilot Experimental Study.},
journal = {Nutrients},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/nu17071108},
pmid = {40218866},
issn = {2072-6643},
support = {2023-PRE-008-Altendorfer//PMU-Research and Innovation Fund/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Alzheimer Disease/microbiology ; *Eicosapentaenoic Acid/pharmacology/administration & dosage ; Pilot Projects ; Mice ; Mice, Transgenic ; *Dietary Supplements ; Female ; Hippocampus/metabolism ; Amyloid beta-Protein Precursor/genetics ; Disease Models, Animal ; *Histocompatibility Antigens Class II/metabolism ; *Genes, MHC Class II/drug effects ; Fatty Acids, Omega-3 ; },
abstract = {Background/Objectives: Neuroinflammation, a hallmark of Alzheimer's disease (AD), is characterized by elevated levels of inflammatory signaling molecules, including cytokines and eicosanoids, as well as increased microglial reactivity, and is augmented by gut microbiota dysbiosis via the gut-brain axis. We conducted a pilot experiment to elucidate the anti-inflammatory effects of dietary omega-3 polyunsaturated fatty acid (ω-3 PUFA) eicosapentaenoic acid (EPA) on the gut microbiota and neuroinflammation. Methods: Female APP/PS1 mice (TG) and non-transgenic littermates (WT), 13-14 months old, were fed a diet supplemented with 0.3% EPA or control chow for 3 weeks. The gut microbiota composition, hippocampal and plasma eicosanoids levels, platelet activation, and microglial phagocytosis, as well as the brain and retinal genes and protein expression, were analyzed. Results: EPA supplementation decreased the percentage of Bacteroidetes and increased bacteria of the phylum Firmicutes in APP/PS1 and WT mice. Inflammatory lipid mediators were elevated in the hippocampus of the TG mice, accompanied by a reduction in the endocannabinoid docosahexaenoyl ethanolamide (DHEA). Dietary EPA did not affect hippocampal lipid mediators, but reduced the levels of arachidonic-derived 5-HETE and N-arachidonoylethanolamine (AEA) in WT plasma. Moreover, EPA supplementation decreased major histocompatibility complex class II (MHCII) gene expression in the retina in both genotypes, and MHCII+ cells in the hippocampus of TG mice. Conclusions: This pilot study showed that short-term EPA supplementation shaped the gut microbiota by increasing butyrate-producing bacteria of the Firmicutes phylum and decreasing Gram-negative LPS-producing bacteria of the Bacteroidetes phylum, and downregulated the inflammatory microglial marker MHCII in two distinct regions of the central nervous system (CNS). Further investigation is needed to determine whether EPA-mediated effects on the microbiome and microglial MHCII have beneficial long-term effects on AD pathology and cognition.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Alzheimer Disease/microbiology
*Eicosapentaenoic Acid/pharmacology/administration & dosage
Pilot Projects
Mice
Mice, Transgenic
*Dietary Supplements
Female
Hippocampus/metabolism
Amyloid beta-Protein Precursor/genetics
Disease Models, Animal
*Histocompatibility Antigens Class II/metabolism
*Genes, MHC Class II/drug effects
Fatty Acids, Omega-3

@article {pmid40218348,
year = {2025},
author = {Du, H and Li, K and Guo, W and Na, M and Zhang, J and Zhang, J and Na, R},
title = {Physiological and Microbial Community Dynamics in Does During Mid-Gestation to Lactation and Their Impact on the Growth, Immune Function, and Microbiome Transmission of Offspring Kids.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070954},
pmid = {40218348},
issn = {2076-2615},
support = {BR22-13-02//Basic scientific research business fee project for universities directly under the Inner Mongolia Autonomous Region/ ; NMGIRT2322//Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {This study investigated changes in physiological processes and rumen microbial communities in does from mid-gestation to lactation and identified potential associations between these physiological changes and the rumen microbiome. Additionally, we studied the transmission mechanisms of microorganisms between the dam and offspring. Our study demonstrates significant changes in maternal physiological metabolism, immune status, and rumen microbiota from mid-pregnancy through lactation. We identified potential associations between these physiological changes and the rumen microbiome. Moreover, the findings highlight that alterations in maternal physiological metabolism and immune status significantly influence the growth and immune development of offspring kids. Additionally, we observed that the maternal microbiota serves as a key source of gastrointestinal microbial communities in young animals, with early colonization of maternally derived microbes in the offspring's gastrointestinal tract playing a role in shaping their immune system development. The results for primary outcomes are as follows: The serum levels of estrogen and progesterone in pregnant does were greater than those observed during lactation, while the concentration of growth hormone, triiodothyronine, and glucose exhibited an upward trend during lactation. During late gestation, the serum IL-10 concentration in does decreased, while the TNF-α concentration increased. Additionally, on day 140 of gestation, does showed a significant decrease in IgG, total protein, and globulin levels. From mid-gestation to lactation, the abundance of dominant phyla and genera, including Firmicutes, Bacteroidetes, Patescibacteria, Bacteroidales_RF16_group, Clostridia_UCG-014, RF39, and Eubacterium_ventriosum_group, in the rumen of does underwent significant changes. LEfSe analysis identified a series of marker microorganisms in the rumen of does at different physiological stages. A correlation was observed between these dominant bacteria and the serum physiological indicators of the does. Notably, rumen volatile fatty acids also exhibited a correlation with serum physiological indicators. In addition, serum physiological indicators of does were significantly correlated with the growth and immune indicators of their kids. Microbiological origin analysis revealed that the gastrointestinal microbiome of kids primarily originated from the rumen, birth canal, and milk of does. Further analysis identified a correlation between the kids' serum immunometric indicators and certain gastrointestinal microorganisms. In particular, the jejunum microbiota of 28-day-old lactating kids, including Alysiella, Neisseria, and Muribaculaceae, showed a significant positive correlation with serum IL-6 and IL-10 levels. Meanwhile, these genera were dominant in the saliva and milk of does, suggesting a direct microbial transfer from dam to offspring. These microbial communities may play a significant role in modulating the metabolism and immune responses of the offspring, thereby influencing their immune system development.},
}

@article {pmid40218330,
year = {2025},
author = {Li, W and Zeng, X and Wang, L and Yin, L and Wang, Q and Yang, H},
title = {Comparative Analysis of Gut Microbiota Diversity Across Different Digestive Tract Sites in Ningxiang Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070936},
pmid = {40218330},
issn = {2076-2615},
support = {2025JJ50141//The Natural Science Foundation Project of Hunan Province/ ; 2022RC3060//Science and Technology Innovation Program of Hunan Province/ ; 24A0044//Hunan Provincial Department of Education key project/ ; },
abstract = {BACKGROUND: Microbial communities in the gastrointestinal tract play a critical role in nutrient absorption, metabolism, and overall health of animals. Understanding the structure and function of tissue-specific microbial communities in Ningxiang pigs is essential for optimizing their growth, development, and nutritional efficiency. However, the diversity and functional roles of microbiota in different nutrient absorption tissues remain underexplored.

METHODS: We collected samples from four key nutrient absorption tissues (NFC: Cecal Content, NFI: Ileal Content, NFL: Colonic Content, NFG: Gastric Content, N = 6) of Ningxiang pigs and performed 16S rRNA gene sequencing to analyze microbial community composition. Bioinformatics analyses included alpha and beta diversity assessments, linear discriminant analysis effect size (LEfSe) for biomarker identification, and PICRUSt2-based functional prediction. Comparative metabolic abundance analysis was conducted to explore functional differences among tissues.

RESULTS: Alpha diversity indices (ACE, Chao1, Simpson, and Shannon) revealed significant differences in microbial richness and evenness among the four tissues. At the phylum level, Firmicutes dominated the microbiota, while Bacteroidota was prominent in NFC and NFL. LEfSe analysis identified tissue-specific dominant microbial groups, such as f_Prevotellaceae in NFC, o_Lactobacillales in NFG, f_Clostridiaceae in NFI, and f_Muribaculaceae in NFL. Functional profiling using PICRUSt2 showed that the microbiota was primarily involved in organismal systems (e.g., aging, digestion), cellular processes (e.g., cell growth, transport), environmental information processing (e.g., signaling), genetic information processing (e.g., transcription, translation), and metabolic regulation (e.g., amino acid and carbohydrate metabolism). Comparative metabolic abundance analysis highlighted distinct functional profiles across tissues, with significant differences observed in pathways related to the immune system, energy metabolism, lipid metabolism, transcriptional and translational regulation, and aging.

CONCLUSIONS: Our findings demonstrate that tissue-specific microbial communities in Ningxiang pigs exhibit distinct structural and functional characteristics, which are closely associated with nutrient absorption and metabolic regulation. These results provide valuable insights into the roles of microbiota in the growth and health of Ningxiang pigs and pave the way for future studies on microbe-mediated nutritional interventions.},
}

@article {pmid40218302,
year = {2025},
author = {Gao, Z and Tian, J and Zhang, Q and Sun, H and Jiang, Q and Zhang, T},
title = {Effects of Dietary Protein and Fat Levels on Growth Performance, Nutrient Digestibility, Serum Indexes, and Rectal Fecal Microbiota of Sika Deer (Cervus nippon) Fawns in Early Wintering Period.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {7},
pages = {},
doi = {10.3390/ani15070908},
pmid = {40218302},
issn = {2076-2615},
support = {CAASASTIP-2021-ISAPS//Agricultural Science and Technology Innovation Program of China/ ; },
abstract = {This study examined the effects of dietary crude protein (CP: 18%, 15%) and crude fat (EE: 8%, 4%) levels, and their interactions, on growth performance, nutrient digestibility, serum indices, and rectal fecal microbiota in sika deer fawns during early wintering. A two-month 2 × 2 factorial experiment was conducted using 32 healthy five-month-old male fawns randomly assigned to four groups: P18E8 (18% CP, 8% EE), P18E4 (18% CP, 4% EE), P15E8 (15% CP, 8% EE), and P15E4 (15% CP, 4% EE). The P18E4 group showed the highest total weight gain and average daily gain (p < 0.05), along with greater apparent digestibility of dry matter, crude protein, calcium, and fiber fractions (p < 0.05). Serum urea content was significantly lower in this group, indicating improved nitrogen utilization (p < 0.05). Dominant fecal microbiota at the phylum level across all groups included Firmicutes_A and Bacteroidota, with the P18E4 group showing a unique genus composition within Bacteroidota, known for enhancing fiber digestion. In summary, a diet with 18% CP and 4% EE optimized growth performance, nutrient digestibility, and gut microbiota composition, providing a strategy for improving the health and productivity of sika deer fawns during overwintering.},
}

@article {pmid40217936,
year = {2025},
author = {Boscia, G and Spataro, F and Desantis, V and Solimando, AG and Vacca, A and Ria, R and Savastano, A},
title = {Ocular Side Effects of Dupilumab: A Comprehensive Overview of the Literature.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072487},
pmid = {40217936},
issn = {2077-0383},
abstract = {Dupilumab, a monoclonal antibody targeting the interleukin (IL)-4 receptor alpha subunit and IL-13, has markedly advanced the treatment of atopic conditions such as dermatitis, asthma, and chronic rhinosinusitis. However, its expanding use has brought increased attention to a range of ocular adverse events-conjunctivitis, blepharitis, keratitis, corneal ulcers, and cicatricial conjunctivitis-that remain underrecognized and frequently underestimated in clinical practice. These manifestations often emerge in patients with atopic dermatitis and display varying severity, posing diagnostic and therapeutic challenges. Rather than isolated phenomena, these effects appear to stem from a complex interplay of goblet cell depletion, mucin deficiency, immune dysregulation, and microbiome alterations, including Demodex proliferation. Current management strategies remain largely empirical, lacking standardized protocols, and are often guided by anecdotal evidence. In this review, we critically appraise the existing literature, synthesize emerging pathogenic hypotheses, and highlight the unmet clinical need for evidence-based treatment algorithms. We advocate for a multidisciplinary approach and future research aimed at elucidating mechanisms, refining risk stratification, and minimizing ocular toxicity without compromising the therapeutic benefits of dupilumab. Furthermore, we intend to provide a more practical and straightforward resource for the reader based on the current literature on approaching the topic.},
}

@article {pmid40217873,
year = {2025},
author = {Cucu, CI and Giurcăneanu, C and Mihai, MM and Andronic, T and Ancuta, I and Popa, MI and Macovei, IS and Popa, LG},
title = {Unraveling the Skin Microbiome in Hidradenitis Suppurativa: Implications for Treatment and Disease Progression.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072424},
pmid = {40217873},
issn = {2077-0383},
support = {Publish, not Perish//Carol Davila University of Medicine and Pharmacy/ ; },
abstract = {Background: Hidradenitis suppurativa (HS) is a chronic, disabling, and disfiguring inflammatory disease with a complex, incompletely elucidated pathogenesis. The role of skin dysbiosis in the development and progression of HS has not yet been clarified. Methods: We performed an observational, prospective culture-based study that included 40 HS patients and analyzed the bacterial load and diversity in HS skin lesions, their correlation with disease severity, and several host and environmental factors. Additionally, we investigated the prevalence of antibiotic resistance and determined the resistance profile of bacterial strains isolated from chronic HS lesions. Results: An impressive number and diversity of bacterial strains were isolated from both superficial and deep HS lesions. 201 aerobic and anaerobic bacterial strains were isolated, polymicrobial growth being detected in the majority of samples. The most frequently isolated bacteria were Staphylococcus epidermidis, Staphylococcus aureus, Staphylococcus lugdunensis, Peptoniphilus spp., and Enterococcus faecalis in superficial lesions and Staphylococcus epidermidis, Staphylococcus aureus, and Corynebacterium tuberculostearicum in deep lesions. A significantly higher bacterial density and diversity was found in male patients, regardless of the affected area and in patients with severe HS. The proportion of bacterial strains resistant to antibiotics was lower in our study (8.95%) compared to the previously reported data. Conclusions: Our findings indicate dysbiosis as a key player in the initiation and maintenance of the inflammatory process in HS. Further large-scale, prospective studies are required to comprehensively characterize the microbiological landscape of HS and shed light on its contribution in the pathogenesis of the disease.},
}

@article {pmid40217801,
year = {2025},
author = {Bekbossynova, M and Saliev, T and Ivanova-Razumova, T and Andossova, S and Kali, A and Myrzakhmetova, G},
title = {Beyond Cholesterol: Emerging Risk Factors in Atherosclerosis.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072352},
pmid = {40217801},
issn = {2077-0383},
support = {BR21881970//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Atherosclerosis remains a leading cause of cardiovascular morbidity and mortality worldwide, traditionally linked to elevated cholesterol levels, particularly low-density lipoprotein cholesterol (LDL-C). However, despite aggressive lipid-lowering strategies, residual cardiovascular risk persists, underscoring the need to explore additional contributing factors. This review examines emerging risk factors beyond cholesterol, including chronic inflammation, gut microbiota composition, oxidative stress, and environmental exposures. Inflammation plays a pivotal role in atherogenesis, with markers such as C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) serving as indicators of disease activity. The gut microbiome, particularly metabolites like trimethylamine N-oxide (TMAO), has been implicated in vascular inflammation and plaque development, while beneficial short-chain fatty acids (SCFAs) demonstrate protective effects. Oxidative stress further exacerbates endothelial dysfunction and plaque instability, driven by reactive oxygen species (ROS) and lipid peroxidation. Additionally, environmental factors, including air pollution, heavy metal exposure, endocrine disruptors, and chronic psychological stress, have emerged as significant contributors to cardiovascular disease. Understanding these novel risk factors offers a broader perspective on atherosclerosis pathogenesis and provides new avenues for targeted prevention and therapeutic interventions.},
}

@article {pmid40217595,
year = {2025},
author = {Batir-Marin, D and Ștefan, CS and Boev, M and Gurău, G and Popa, GV and Matei, MN and Ursu, M and Nechita, A and Maftei, NM},
title = {A Multidisciplinary Approach of Type 1 Diabetes: The Intersection of Technology, Immunotherapy, and Personalized Medicine.},
journal = {Journal of clinical medicine},
volume = {14},
number = {7},
pages = {},
doi = {10.3390/jcm14072144},
pmid = {40217595},
issn = {2077-0383},
abstract = {Background: Type 1 diabetes (T1D) is a chronic autoimmune disorder characterized by the destruction of pancreatic β-cells, leading to absolute insulin deficiency. Despite advancements in insulin therapy and glucose monitoring, achieving optimal glycemic control remains a challenge. Emerging technologies and novel therapeutic strategies are transforming the landscape of T1D management, offering new opportunities for improved outcomes. Methods: This review synthesizes recent advancements in T1D treatment, focusing on innovations in continuous glucose monitoring (CGM), automated insulin delivery systems, smart insulin formulations, telemedicine, and artificial intelligence (AI). Additionally, we explore biomedical approaches such as stem cell therapy, gene editing, immunotherapy, gut microbiota modulation, nanomedicine-based interventions, and trace element-based therapies. Results: Advances in digital health, including CGM integration with hybrid closed-loop insulin pumps and AI-driven predictive analytics, have significantly improved real-time glucose management. AI and telemedicine have enhanced personalized diabetes care and patient engagement. Furthermore, regenerative medicine strategies, including β-cell replacement, CRISPR-based gene editing, and immunomodulatory therapies, hold potential for disease modification. Probiotics and microbiome-targeted therapies have demonstrated promising effects in maintaining metabolic homeostasis, while nanomedicine-based trace elements provide additional strategies to regulate insulin sensitivity and oxidative stress. Conclusions: The future of T1D management is shifting toward precision medicine and integrated technological solutions. While these advancements present promising therapeutic avenues, challenges such as long-term efficacy, safety, accessibility, and clinical validation must be addressed. A multidisciplinary approach, combining biomedical research, artificial intelligence, and nanotechnology, will be essential to translate these innovations into clinical practice, ultimately improving the quality of life for individuals with T1D.},
}

@article {pmid40217575,
year = {2025},
author = {Ochi, T and Fujiki, R and Fukuyo, M and Rahmutulla, B and Nakagawa, T and Ota, M and Ikeda, JI and Matsui, Y and Yoshino, I and Suzuki, H and Kaneda, A},
title = {Association of Intratumoral Bacterial Abundance With Lung Cancer Prognosis in Chiba University Hospital Cohort.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.70080},
pmid = {40217575},
issn = {1349-7006},
support = {22zf0127008s0301//Japan Agency for Medical Research and Development/ ; //Chiba University/ ; //Chiba Foundation for Health Promotion and Disease Prevention/ ; },
abstract = {The relationship between cancer prognosis and intratumoral microbiome has recently gained attention. Regarding lung cancer, most studies have focused on bacteria outside tumors, such as sputum or lavage fluid, with few examining intratumoral bacteria and their impact on prognosis. In this study, we extracted DNA from lung tumor samples of 507 patients undergoing surgery at Chiba University Hospital and quantified intratumoral bacterial abundance using bacteria-specific PCR primers. Bacteria were detected in 77.1% of cases, and bacterial abundance was significantly higher in lung adenocarcinoma than in squamous cell carcinoma. Patients were categorized into three groups (High, Low, and Very-Low) based on bacterial abundance, and associations with clinicopathological factors were analyzed. In lung squamous cell carcinoma, higher bacterial abundance was significantly associated with worse recurrent-free survival and overall survival and was found to be a poor prognostic factor independent of pathological tumor stage. In conclusion, intratumoral bacterial abundance was found in the majority of lung cancer tissues, with variations based on pathology. This abundance may serve as a useful marker for stratifying lung squamous cell carcinoma with distinct prognoses.},
}

@article {pmid40217292,
year = {2025},
author = {Diop, K and Mbaye, B and Nili, S and Filin, A and Benlaifaoui, M and Malo, J and Renaud, AS and Belkaid, W and Hunter, S and Messaoudene, M and Lee, KA and Elkrief, A and Routy, B},
title = {Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {21},
pmid = {40217292},
issn = {1757-4749},
abstract = {BACKGROUND: The gut microbiome represents a novel biomarker for melanoma and non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Gut microbiome metagenomics profiling studies of patients treated with immunotherapy identified bacteria associated with ICI efficacy, while others have been linked to resistance. However, limitations of metagenomics sequencing, such as complex bioinformatic processing requirements, necessity of a threshold for positive detection, and the inability to detect live organisms, have hindered our ability to fully characterize the gut microbiome. Therefore, combining metagenomics with high-throughput culture-based techniques (culturomics) represents an ideal strategy to fully characterize microbiome composition to more robustly position the microbiome as a biomarker of response to ICI.

METHODS: We performed culturomics using fecal samples from 22 patients from two academic centres in Canada and the United Kingdom with NSCLC and cutaneous melanoma treated with ICI (cancer group), comparing their microbiome composition to that of 7 healthy volunteers (HV), along with matching shotgun metagenomics sequencing.

RESULTS: For culturomics results, 221 distinct species were isolated. Among these 221 distinct species, 182 were identified in the cancer group and 110 in the HV group. In the HV group, the mean species richness was higher compared to the cancer group (34 vs. 18, respectively, p = 0.002). Beta diversity revealed separate clusters between groups (p = 0.004). Bifidobacterium spp. and Bacteroides spp. were enriched in HV, while cancer patients showed an overrepresentation of Enterocloster species, as well as Veillonella parvula. Next, comparing cancer patients' clinical outcomes to ICI, we observed that among the 20 most abundant bacteria present in non-responder patients, 2 belonged to the genus Enterocloster, along with an enrichment of Hungatella hathewayi and Cutibacterium acnes. In contrast, responders to ICI exhibited a predominance of Bacteroides spp. In NSCLC patients, metagenomics analysis revealed that of the 154 bacteria species isolated through culturomics, 61/154 (39%) were also identified by metagenomics sequencing. Importantly, 94 individual species were uniquely detected by culturomics.

CONCLUSION: These findings highlight that culturomics and metagenomics can serve as complementary tools to characterize the microbiome in patients with cancer. This integrated approach uncovers specific microbiome signatures that differentiate HV from cancer patients, and identifies specific species associated with therapy response and resistance.},
}

@article {pmid40217129,
year = {2025},
author = {Quinn-Bohmann, N and Carr, AV and Diener, C and Gibbons, SM},
title = {Moving from genome-scale to community-scale metabolic models for the human gut microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40217129},
issn = {2058-5276},
support = {R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; },
abstract = {Metabolic models of individual microorganisms or small microbial consortia have become standard research tools in the bioengineering and systems biology fields. However, extending metabolic modelling to diverse microbial communities, such as those in the human gut, remains a practical challenge from both modelling and experimental validation perspectives. In complex communities, metabolic models accounting for community dynamics, or those that consider multiple objectives, may provide optimal predictions over simpler steady-state models, but require a much higher computational cost. Here we describe some of the strengths and limitations of microbial community-scale metabolic models and argue for a robust validation framework for developing personalized, mechanistic and accurate predictions of microbial community metabolic behaviours across environmental contexts. Ultimately, quantitatively accurate microbial community-scale metabolic models could aid in the design and testing of personalized prebiotic, probiotic and dietary interventions that optimize for translationally relevant outcomes.},
}