@article {pmid40335388,
year = {2025},
author = {Dwivedi, SL and Vetukuri, RR and Kelbessa, BG and Gepts, P and Heslop-Harrison, P and Araujo, ASF and Sharma, S and Ortiz, R},
title = {Exploitation of rhizosphere microbiome biodiversity in plant breeding.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.04.004},
pmid = {40335388},
issn = {1878-4372},
abstract = {Climate change-induced stresses are perceived by plants at the root-soil interface, where they are alleviated through interactions between the host plant and the rhizosphere microbiome. The recruitment of specific microbiomes helps mitigate stress, increases resistance to pathogens, and promotes plant growth, development, and reproduction. The structure of the rhizosphere microbiome is shaped by crop domestication and variations in ploidy levels. Here we list key genes that regulate rhizosphere microbiomes and host genetic traits. We also discuss the prospects for rigorous analysis of symbiotic interactions, research needs, and strategies for systematically utilizing microbe-crop interactions to improve crop performance. Finally, we highlight challenges of maintaining live rhizosphere microbiome collections and mining heritable variability to enhance interactions between host plants and their rhizosphere microbiomes.},
}

@article {pmid40335161,
year = {2025},
author = {Mela, V and Heras, V and Iesmantaite, M and García-Martín, ML and Bernal, M and Posligua-García, JD and Subiri-Verdugo, A and Martínez-Montoro, JI and Gómez-Pérez, AM and Banderas, B and Moreno Indias, I and Tinahones, FJ},
title = {Microbiota fasting-related changes ameliorate cognitive decline in obesity and boost ex vivo microglial function through the gut-brain axis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335353},
pmid = {40335161},
issn = {1468-3288},
abstract = {BACKGROUND: Obesity-related cognitive decline is linked to gut microbiota dysbiosis, with emerging evidence suggesting that dietary interventions may ameliorate cognitive impairment via gut-brain axis modulation. The role of microglial cells in this process remains underexplored.

OBJECTIVE: To investigate how diet-induced changes in gut microbiota influence cognitive function in individuals with obesity and their microglial activity, and to determine the impact of specific dietary interventions.

DESIGN: This study included 96 participants with obesity who were randomised into three dietary intervention groups: Mediterranean diet (Med), alternate-day fasting (ADF) and ketogenic diet (Keto). Cognitive performance and microbiota composition were assessed pre-intervention and post-intervention. The effects of microbiota-related changes on microglial function were further evaluated in mice models through faecal transplantation and in vitro model with microbiota exosome treatment.

RESULTS: Both the Keto and ADF groups demonstrated significant weight loss, but cognitive performance improved most notably in the ADF group, in association with reduced inflammation. Diet-related microbiota composition was correlated with the cognitive outcomes in the human study. Mice models confirmed that the cognitive benefits of ADF were microbiota-dependent and linked to enhanced microglial phagocytic capacity and reduced inflammation, accompanied by changes in microglia morphology.

CONCLUSION: Fasting-induced modifications in gut microbiota contribute to cognitive improvement in individuals with obesity, with microglial cells playing a crucial mediatory role. Among the interventions, ADF most effectively enhanced microglial function and cognitive performance, suggesting its potential as a therapeutic strategy for obesity-related cognitive decline. Further studies are required to fully elucidate the underlying mechanisms.

TRIAL REGISTRATION NUMBER: NCT04453150.},
}

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

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

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

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

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

@article {pmid40335047,
year = {2025},
author = {Liaquat, M and Minihane, AM and Vauzour, D and Pontifex, MG},
title = {The gut microbiota in menopause: Is there a role for prebiotic and probiotic solutions?.},
journal = {Post reproductive health},
volume = {},
number = {},
pages = {20533691251340491},
doi = {10.1177/20533691251340491},
pmid = {40335047},
issn = {2053-3705},
abstract = {The gut microbiota, comprising a diverse array of microorganisms in the gastrointestinal tract, has emerged as a key player in human health. Emerging research indicates that this gut microbial composition is influenced by sex. These sex differences are not necessarily static and likely alter across the life course in response to several factors including changing hormone profile. As such, the menopause transition-a pivotal phase in female ageing in which the hormone profile changes dramatically is receiving increasing attention. Declining estrogen which occurs during menopause appears to influence the microbiota, which may in turn contribute to menopause-related conditions such as weight gain, bone health, cancer risk and cognitive health. The modulation of estrogen through the gut's 'estrobolome', a collection of bacterial genes involved in estrogen metabolism, may offer explanation for some of the interindividual differences observed during menopause (e.g. length, symptoms and disease risk). Therapeutic modulation of the gut microbiota therefore represents a potential approach towards managing menopausal symptoms. Indeed, prebiotics and probiotics such as Lactobacillus have been shown to increase bacterial diversity and improve metabolic and overall health in menopausal women. However, evidence remains limited regarding the specific underlying mechanisms, highlighting an urgent need for a research focus in the area. This review summarizes the current understanding of the gut microbiota's role in menopausal health and the potential of prebiotics and probiotics as therapeutic interventions. Further research into gut microbiota modulation may enable more effective, personalised treatments for menopause-associated health challenges, and supporting women's health into older ages.},
}

@article {pmid40334798,
year = {2025},
author = {Zhu, X and Chen, L and Yang, P and Luo, S and Teng, M and Zhu, W and Li, Y and Zhao, D and Wang, N and Chen, X and Cheng, M and Tu, H and Huang, W and Yang, F and Wang, L and Liu, X and Ning, K},
title = {Microbiome catalog and dynamics of the Chinese liquor fermentation process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132620},
doi = {10.1016/j.biortech.2025.132620},
pmid = {40334798},
issn = {1873-2976},
abstract = {Fermented food remains poorly understood, largely due to the lack of knowledge about microbes in food fermentation. Here, this study constructed Moutai Fermented Grain Catalog (MTFGC), a representative liquor fermented by one of the most complex fermentations. MTFGC comprised 8,379,551 non-redundant genes and 5,159 metagenome-assembled genomes, with 20% species and 20% genes being novel. Additionally, 25,625 biosynthetic gene clusters (BGCs) and 28 BGC-enriched species were identified. Moreover, the microbial community assembly was deterministic, with significant species and gene changes in early fermentation stages, while stabilizing in later stages. Further BGC-knockout experiments verified Bacillus licheniformis, a BGC-enriched species, employed its BGCs for synthesizing the aroma-related lipopeptide lichenysin. This study has established the largest genetic resource for fermented food, uncovering its uniqueness and high metabolic potential. These findings facilitate the transition potential from traditional fermentation to precision-driven synthetic biology in food systems.},
}

@article {pmid40334786,
year = {2025},
author = {Zhu, Z and Xue, B and Li, H and Wang, X and Li, Y and Huang, J and Cai, S and Zeng, X and Chen, M and Zhang, S and Chen, F and Cai, C and Zeng, X},
title = {Maternal tryptophan supplementation enhances sow reproductive performance by influencing hormones, tryptophan metabolism and gut microbiome.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.04.031},
pmid = {40334786},
issn = {1541-6100},
abstract = {BACKGROUND: Enhancing early embryo survival rate is important for increasing sow reproductive efficiency. Whether and how tryptophan influences early embryo survival and pregnancy outcomes in sows remains unknown.

OBJECTIVE: The objective of this study was to investigate the effects of dietary tryptophan supplementation on the reproductive performance of sows.

METHODS: A total of 128 multiparous Large White × Landrace sows were randomly assigned to four groups including the control group (dietary tryptophan level was 0.18% from weaning to estrus and 0.10% from d 1 to d 28 of pregnancy) or the low, medium, and high dose of tryptophan supplementation groups (dietary tryptophan levels were 0.27%, 0.36%, and 0.45% from weaning to estrus and 0.15%, 0.20%, and 0.25% from d 1 to d 28 of pregnancy). Primary porcine granulosa cells were isolated from porcine ovaries and treated with selected tryptophan metabolites to assess hormone levels in the cell supernatant.

RESULTS: Compared with the control group, dietary high levels of tryptophan group increased the litter weight (P < 0.05) and showed an increasing trend in the born alive per litter (P = 0.06). Serum concentration of progesterone and estradiol and levels of tryptophan, kynurenine, xanthurenic acid, 2-aminobenzoic acid, and indoleamine 2,3-dioxygenase on d 28 of pregnancy was increased in the high level of tryptophan group (P < 0.05). In vitro experiments using primary porcine granulosa cell culture showed that tryptophan and 2-aminobenzoic acid increased progesterone and estradiol levels in the cell supernatant (P < 0.05). Dietary tryptophan supplementation increased the abundances of fecal beneficial bacteria such as Hydrogenoanaerobacterium and Lachnospiraceae in sows (P < 0.05).

CONCLUSIONS: Dietary tryptophan supplementation may enhance the pregnancy outcome of sows through the increase of tryptophan metabolites to strengthen steroid hormone secretion and the abundances of beneficial microbes.},
}

@article {pmid40334619,
year = {2025},
author = {Shibahara, T and Temizoz, B and Egashira, S and Hosomi, K and Park, J and Surucu, N and Björk, A and Sag, E and Doi, T and Kisla Ekinci, RM and Balci, S and Versnel, MA and Kunisawa, J and Yamamoto, M and Hayashi, T and Ito, S and Kamiyama, Y and Kobiyama, K and Katsikis, PD and Coban, C and Gursel, M and Ozen, S and Nishida, S and Kumanogoh, A and Ishii, KJ},
title = {Microbial dysbiosis fuels STING-driven autoinflammation through cyclic dinucleotides.},
journal = {Journal of autoimmunity},
volume = {154},
number = {},
pages = {103434},
doi = {10.1016/j.jaut.2025.103434},
pmid = {40334619},
issn = {1095-9157},
abstract = {Aberrant activation of the stimulator of interferon genes (STING) pathway is a hallmark of autoinflammatory disorders such as STING-associated vasculopathy with onset in infancy (SAVI), characterized by systemic inflammation affecting blood vessels, skin, and lungs. Despite its clinical significance, the mechanisms linking STING activation to disease pathology remain poorly defined. In this study, we demonstrated that SAVI mice harboring the N153S STING mutation exhibit diverse disease phenotypes, with a subset developing severe colitis and diarrhea alongside exacerbated systemic inflammation. These diarrheal SAVI mice showed pronounced dysbiosis, marked by reduced short-chain fatty acid-producing bacteria and an enrichment of segmented filamentous bacteria. This microbial imbalance was accompanied by elevated levels of both microbial and host-derived cyclic dinucleotides (CDNs), potent activators of the STING pathway. Notably, antibiotic treatment ameliorated inflammation, underscoring the role of dysbiosis in driving STING-mediated autoinflammation. Furthermore, in SAVI patients, elevated systemic microbial and host-derived CDNs were observed. In conditions such as systemic lupus erythematosus (SLE)-a heterogeneous autoimmune disease with potential STING involvement-systemic microbial CDNs were significantly correlated with disease biomarkers, including type I interferon scores and anti-dsDNA antibodies. In contrast, no such correlations were observed in STING-independent conditions like rheumatoid arthritis (RA). Importantly, this study highlights that both microbial and host-derived CDNs are key drivers of STING activation, suggesting that personalized treatment strategies could target cGAS or the microbiome based on a patient's specific CDN profile. These findings position systemic CDNs as valuable biomarkers and therapeutic targets for STING-driven diseases.},
}

@article {pmid40334594,
year = {2025},
author = {Zhang, B and Yang, R and Liu, Y and Guo, J and Yang, J and Qin, X and Wang, S and Liu, J and Yang, X and Zhang, W and Liu, G and Chen, T},
title = {From glacier forelands to human settlements: Patterns, environmental drivers, and risks of antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138455},
doi = {10.1016/j.jhazmat.2025.138455},
pmid = {40334594},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) are biological pollutants widely present in glaciers, such as ice, snow, and melt water. However, it remains unclear whether ARGs in glaciers influence their distribution in human settlements within the glacier basins. Therefore, we investigated the distribution pattern and driving factors of ARGs in the Laohugou glacier basins on the Tibetan Plateau. Using high-throughput quantitative PCR, the total abundance of ARGs in the Laohugou glacier basins ranged from 7.53 × 10[6] to 1.83 × 10[9] copies/g, including 128 detected ARGs across 11 classes, with aminoglycoside resistance genes being the dominant group. The abundance of ARGs exhibited a U-shaped pattern along the elevational gradient, with higher levels in glacier regions and human settlements, and the lowest abundance at mid-elevations. While glacier melting and anthropogenic disturbance are likely major contributors to this pattern, other potential mechanisms may also be involved, such as elevation-dependent microbial community composition, atmospheric deposition and release of legacy ARGs from melting permafrost and glacial ice. Together, these processes likely interact to shape the observed ARG pattern in this alpine watershed. We further verified that the distribution of ARGs was strongly correlated with microbial community structure, especially bacterial communities (r > 0.50; p < 0.05). Network analysis showed that Nitrolancea negatively correlated with several core ARGs, suggesting its potential role in regulating the spread of ARGs. Random forest analysis and structural equation modeling (SEM) indicated that, after accounting for various driving factors, organic matter and bacterial biomass were the primary drivers of increased ARG abundance. This study provides a foundation for assessing the risks of ARGs in glacier basins under global climate change, offering insights into risk mitigation strategies and guiding future ecological and public health research.},
}

@article {pmid40334428,
year = {2025},
author = {Gu, S and Chen, C and Wang, J and Wang, Y and Zhao, L and Xiong, Z and Zhang, H and Deng, T and Pan, Q and Zheng, Y and Li, Y},
title = {Camellia Japonica Radix modulates gut microbiota and 9(S)-HpODE-mediated ferroptosis to alleviate oxidative stress against MASLD.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {143},
number = {},
pages = {156806},
doi = {10.1016/j.phymed.2025.156806},
pmid = {40334428},
issn = {1618-095X},
abstract = {BACKGROUND: Camellia japonica radix (CJR), derived from the root of Camellia japonica L., has the potential to function as an herbal tea substitute for the prevention and intervention of metabolic dysfunction-associated steatotic liver disease (MASLD). It can provide systemic therapeutic benefits, boast a favorable safety profile, facilitate convenient consumption, and support long-term applicability. Despite its potential, research on CJR remains limited.

PURPOSE: The aim of this study aims is to elucidate the therapeutic mechanisms of CJR in MASLD, thereby providing evidence to support its clinical application.

METHODS: The therapeutic effects of CJR were evaluated using a water-supplementation model in MASLD mice. Integrated microbiome, transcriptome, proteome, and metabolome analyses were employed to comprehensively explore the mechanisms involved. A drug-target pull-down assay was performed to identify specific protein targets of small molecule metabolites in vitro. Fecal microbiota transplantation in antibiotic-treated ABX mice was conducted to confirm the critical role of gut microbiota and its metabolites. Furthermore, customized medicated feed supplemented with linoleic acid was used to explore the intervention effect of its metabolite, 9(S)-HpODE, as well as to evaluate its dietary intervention potential.

RESULTS: This present study explicitly elucidates the efficacy of CJR extract in alleviating hepatic inflammation and steatosis in a MASLD model mice, with its pharmacological mechanism associated with gut microbiota, linoleic acid metabolism, and GPX4-mediated ferroptosis. Notably, 9(S)-HpODE was discovered to be a key metabolite of linoleic acid, which could target both KEAP1 and SLC7A11, bidirectionally regulating GPX4-mediated ferroptosis, while acting as a signaling molecule at low doses to induce redox adaptation via oxidative preconditioning, thus ameliorating oxidative stress in MASLD.

CONCLUSION: Our findings indicate that both CJR and linoleic acid exhibit significant potential as dietary interventions for the management of MASLD, offering promising avenues for future research and clinical application.},
}

@article {pmid40334425,
year = {2025},
author = {Sun, W and Zhang, C and Xu, J and Zhao, M and Li, P},
title = {Natural small-molecule compounds targeting Helicobacter pylori virulence factors: A promising strategy for overcoming antibiotic resistance.},
journal = {Biochemical and biophysical research communications},
volume = {768},
number = {},
pages = {151877},
doi = {10.1016/j.bbrc.2025.151877},
pmid = {40334425},
issn = {1090-2104},
abstract = {Helicobacter pylori (H. pylori) infection is an important causal factor of gastritis, peptic ulcer, and gastric cancer. High infection rates and the increasing challenge of antibiotic resistance worldwide have prompted an urgent need to develop novel therapeutic options and antimicrobial agents. This review focuses on the potential of natural small-molecule compounds as novel anti-H. pylori agents-a promising approach that mitigates the risk of resistance development and maintains the microbiome's ecological balance. We detail how H. pylori virulence factors, including urease, CagA, VacA, and biofilm, contribute to pathogenicity and underline the reassuring fact that naturally derived compounds sourced from plants and microorganisms have shown remarkable efficacy in inhibiting these virulence factors. Some compounds also exhibit synergistic effects with conventional antibiotics, potentially overcoming challenges associated with resistant strains. Furthermore, we discuss recent advancements in identifying novel drug targets within the H. pylori virulence spectrum, offering insights into future directions for research and development in H. pylori therapy.},
}

@article {pmid40334224,
year = {2025},
author = {Pope, Q and Varma, R and Tataru, C and David, MM and Fern, X},
title = {Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data.},
journal = {PLoS computational biology},
volume = {21},
number = {5},
pages = {e1011353},
doi = {10.1371/journal.pcbi.1011353},
pmid = {40334224},
issn = {1553-7358},
abstract = {We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional external labels) to capture the interactions among different microbial taxa and the common compositional patterns in microbial communities. The learned model produces contextualized taxon representations that allow a single microbial taxon to be represented differently according to the specific microbial environment in which it appears. The model further provides a sample representation by collectively interpreting different microbial taxa in the sample and their interactions as a whole. We demonstrate that, while our sample representation performs comparably to baseline models in in-domain prediction tasks such as predicting Irritable Bowel Disease (IBD) and diet patterns, it significantly outperforms them when generalizing to test data from independent studies, even in the presence of substantial distribution shifts. Through a variety of analyses, we further show that the pre-trained, context-sensitive embedding captures meaningful biological information, including taxonomic relationships, correlations with biological pathways, and relevance to IBD expression, despite the model never being explicitly exposed to such signals.},
}

@article {pmid40333219,
year = {2025},
author = {Wang, Y and Waters, AK and Basalirwa, G and Ssetaala, A and Mpendo, J and Namuniina, A and Keneema, E and Kiiza, D and Kyosiimire-Lugemwa, J and Mayanja, Y and Okech, B and Kiwuwa-Muyingo, S},
title = {Impact of Schistosoma mansoni Infection on the Gut Microbiome and Hepatitis B Vaccine Immune Response in Fishing Communities of Lake Victoria, Uganda.},
journal = {Vaccines},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vaccines13040375},
pmid = {40333219},
issn = {2076-393X},
abstract = {OBJECTIVE: Schistosoma mansoni (S. mansoni) infection is endemic in Ugandan fishing communities. We investigated its potential impact on Hepatitis B (Hep B) vaccine responses and its role in mediating the association between the gut microbiome and long-term effectiveness of the vaccine.

METHODS: Participants were tested for S. mansoni infections at baseline and received the Hep B vaccine at baseline, month 1, and month 6. Those with infections were treated. Stool samples were collected at baseline and analyzed using 16S rRNA sequencing. The Wilcoxon rank-sum test was used to compare alpha diversity between groups. A linear regression model was applied to estimate the association between one-year Hep B vaccine responses and the baseline gut microbiome by infection status, adjusting for age and sex.

RESULTS: A total of 107 participants were included (44 from the fishing community and 63 from the Kampala community). There was no significant difference in microbiome composition by location or infection status at baseline or discharge. In the linear regression analysis, S. mansoni infection (β = 1.24, p = 0.025) and a higher alpha diversity (β = 0.001, p = 0.07) were associated with higher Hep B vaccine responses, while older age was associated with a lower Hep B vaccine response (β = -0.06, p = 0.0013).

CONCLUSIONS: S. mansoni infection status before vaccination may modify the association between the gut microbiome and Hep B vaccine response. Potential interventions could focus on infection control as well as improving microbiome richness before implementing vaccine programs in fishing communities.},
}

@article {pmid40333164,
year = {2025},
author = {Wu, J and Peng, Y and Tian, R and Yu, H and Hu, H and Huang, Q and Xu, Y and Liu, L and Pan, H},
title = {Investigating Correlation Between Gut Microbiota and Rheumatoid Arthritis Subtypes by Mendelian Randomization.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040385},
pmid = {40333164},
issn = {2076-0817},
support = {82305172//National Natural Science Foundation of China/ ; SZ2022KF03//Technology Research Projects of State Key Laboratory of Dampness Syndrome of Chinese Medicine/ ; 2020B1515130005//Guangdong Basic and Applied Basic Research Foundation/ ; },
mesh = {*Arthritis, Rheumatoid/microbiology/genetics ; *Gastrointestinal Microbiome ; Humans ; *Mendelian Randomization Analysis ; Genome-Wide Association Study ; Bacteria/classification/genetics ; },
abstract = {Background: Previous studies have demonstrated that the gut microbiota (GM) and rheumatoid arthritis (RA) are significantly associated, but the causal relationship has not been fully elucidated. Methods: We investigated the association between GM and RA using Mendelian randomization (MR) with two independent samples. Our study aimed to determine the causal relationship between gut microbiota and RA, including its seronegative and seropositive subtypes. Using data from a genome-wide association study (GWAS), we identified instrumental variables for 211 gut bacteria types. We then analyzed the FinnGen GWAS dataset, which included 3877 seronegative RA cases and 285,035 controls, along with 4290 seropositive RA cases and 368,362 controls, employing the inverse variance weighted (IVW) method and rigorous tests for pleiotropy and heterogeneity to ensure reliability. Results: The IVW results revealed that Prevotella 9, Sutterella, and Christensenellaceae R.7 exhibited an adverse correlation with seronegative RA (p < 0.05). Additionally, Lachnospira, Slackia, Roseburia, Barnesiella, and Prevotella 7 were associated with a reduced occurrence of seropositive RA (p < 0.05). Conversely, Ruminococcaceae UCG002 and Ruminococcus gauvreauii were linked to an increased susceptibility to seropositive RA (p < 0.05). Notably, no significant heterogeneity (p > 0.05) or pleiotropy (p > 0.05) was detected in the analysis of the significant MR estimates. Conclusions: Our study suggested significant associations between several gut bacteria and RA subtypes, indicating a potential microbial influence on RA development. These findings enhance our understanding of the gut-joint axis in RA and highlight promising targets for future microbiota-based therapies.},
}

*Arthritis, Rheumatoid/microbiology/genetics
*Gastrointestinal Microbiome
Humans
*Mendelian Randomization Analysis
Genome-Wide Association Study
Bacteria/classification/genetics

@article {pmid40333159,
year = {2025},
author = {Gao, Y and Lou, Y and Hui, Y and Chen, H and Sang, H and Liu, F},
title = {Characterization of the Gut Microbiota in Patients with Psoriasis: A Systematic Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040358},
pmid = {40333159},
issn = {2076-0817},
support = {22LCYY-QH10//Jinling Hospital/ ; },
mesh = {Humans ; *Psoriasis/microbiology/therapy ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Dysbiosis/microbiology/therapy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Psoriasis is a prevalent and persistent inflammatory disorder with systemic manifestations. Emerging evidence implicates the gut microbiota in regulating inflammatory responses, metabolic pathways, and immune homeostasis. This review synthesizes current evidence on gut microbiota dysbiosis in psoriasis and evaluates the therapeutic potential of probiotics and fecal microbiota transplantation (FMT) in disease management. Method: Following PRISMA guidelines, we systematically reviewed studies investigating gut microbiome profiles in psoriasis through the MEDLINE, EMBASE, and Web of Science databases (January 2015-December 2024). Included studies utilized 16S rRNA gene sequencing or metagenomic analyses for microbial characterization. Results: Comparative analyses revealed distinct gut microbiota patterns in psoriasis patients compared with healthy controls, although specific microbial signatures exhibited inconsistencies across studies. Notably, interventions modulating gut microbiota composition-particularly probiotic supplementation-demonstrated measurable improvements in psoriasis severity scores and inflammatory markers. Conclusions: Gut microbiome modulation represents a promising therapeutic strategy for psoriasis; however, current evidence highlights the need for standardized microbial analysis methodologies and larger longitudinal studies to establish causality. Future research should prioritize the functional characterization of microbiota-host interactions to optimize therapeutic applications.},
}

Humans
*Psoriasis/microbiology/therapy
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Dysbiosis/microbiology/therapy
RNA, Ribosomal, 16S/genetics

@article {pmid40333133,
year = {2025},
author = {Niculescu, AG and Mitache, MM and Grumezescu, AM and Chifiriuc, MC and Mihai, MM and Tantu, MM and Tantu, AC and Popa, LG and Grigore, GA and Cristian, RE and Popa, MI and Vrancianu, CO},
title = {From Microbial Ecology to Clinical Challenges: The Respiratory Microbiome's Role in Antibiotic Resistance.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040355},
pmid = {40333133},
issn = {2076-0817},
support = {CNFIS-FDI-2024-F-0484 INOVEX//University of Bucharest/ ; Pillar III, Component C9/Investment no. 8 (I8) - contract CF 68//; Ministry of Research, Innovation and Digitalization through the National Recovery and Resilience Plan (PNRR) of Romania/ ; project no. 23020101, Contract no. 7N from 3 January 2023//The core program within the National Research Development and Innovation Plan, 2022-2027', carried out with the support of the Ministry of Research, Innovation and Digitalization (MCID)/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Respiratory Tract Infections/microbiology/drug therapy ; *Drug Resistance, Microbial ; Probiotics ; *Drug Resistance, Bacterial ; *Respiratory System/microbiology ; },
abstract = {Antibiotic resistance represents a growing public health threat, with airborne drug-resistant strains being especially alarming due to their ease of transmission and association with severe respiratory infections. The respiratory microbiome plays a pivotal role in maintaining respiratory health, influencing the dynamics of antibiotic resistance among airborne pathogenic microorganisms. In this context, this review proposes the exploration of the complex interplay between the respiratory microbiota and antimicrobial resistance, highlighting the implications of microbiome diversity in health and disease. Moreover, strategies to mitigate antibiotic resistance, including stewardship programs, alternatives to traditional antibiotics, probiotics, microbiota restoration techniques, and nanotechnology-based therapeutic interventions, are critically presented, setting an updated framework of current management options. Therefore, through a better understanding of respiratory microbiome roles in antibiotic resistance, alongside emerging therapeutic strategies, this paper aims to shed light on how the global health challenges posed by multi-drug-resistant pathogens can be addressed.},
}

Humans
*Microbiota/drug effects
Anti-Bacterial Agents/pharmacology/therapeutic use
*Respiratory Tract Infections/microbiology/drug therapy
*Drug Resistance, Microbial
Probiotics
*Drug Resistance, Bacterial
*Respiratory System/microbiology

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

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

@article {pmid40333040,
year = {2025},
author = {Galaviz-Silva, L and Rodríguez de la Fuente, AO and Gomez-Flores, R and Ibarra-Gámez, JC and Luna-Cruz, IE and Elizondo-Luevano, JH and Sánchez-Díaz, R and Molina Garza, ZJ},
title = {Characterization of Microbiome Diversity in the Digestive Tract of Penaeus vannamei Fed with Probiotics and Challenged with Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/pathogens14040320},
pmid = {40333040},
issn = {2076-0817},
support = {3157//CONAHCYT/ ; },
mesh = {Animals ; *Penaeidae/microbiology ; *Probiotics/administration & dosage ; *Vibrio parahaemolyticus ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Hepatopancreas/microbiology/pathology ; *Gastrointestinal Tract/microbiology ; *Vibrio Infections/microbiology/veterinary ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The microbiome of the shrimp's digestive tract shows differences between healthy and acute hepatopancreatic necrosis disease (AHPND)-affected shrimp. The present study aimed to evaluate the impact of probiotic consumption on the microbial community in experimentally AHPND-infected shrimp. Effective probiotics (EPs) Vibrio alginolyticus (Va32A), V. campbellii (VcHA), and Bacillus pumilus (BPY100) and non-effective probiotics (NEPs) B. pumilus (Bp43, and BpY119), were employed in bioassays with Penaeus vannamei and challenged with AHPND-causing V. parahaemolyticus (VpAHPND). Stomach (Sto), intestine (Int), and hepatopancreas (Hep) were analyzed by metabarcoding (16S rRNA gene) to characterize the microbiome and biomarkers. Hep-VcHA showed the highest alpha diversity (Shannon index = 5.88; 166 ASVs), whereas the lowest was for Hep-Bp43 (2.33; 7 ASVs). Proteobacteria, Actinobacteria, Bacteroidetes, and Saccharibacteria were the most abundant phyla. The relative abundance of Vibrio sp. was the highest in the Hep and Int of Bp43, BPY119 and the positive control, followed by Rhodobacteraceae in the EP group. Principle coordinate analysis (PCoA) showed a cluster grouped negative (Sto and Hep) control with almost all organs in the EP group causing 28.79% of the variation. The core microbiome of EP was mainly represented by Rhodobacteraceae, Caldilineaceae, Celeribacter indicus, Illumatobacter, Microbacterium, Ruegeria atlantica, Saccharibacteria sp., Shimia biformata, and Thalassobius mediterraneus, whose relative abundance was enriched by probiotics, which may explain their protective roles against VpAHPND, whereas the low survival in the NEP group was associated with a higher diversity of Vibrio spp. Our results present an ecosystem-friendly alternative based on beneficial microorganisms to prevent and control AHPND and probably other bacterial diseases in shrimp farming.},
}

Animals
*Penaeidae/microbiology
*Probiotics/administration & dosage
*Vibrio parahaemolyticus
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Hepatopancreas/microbiology/pathology
*Gastrointestinal Tract/microbiology
*Vibrio Infections/microbiology/veterinary
Bacteria/classification/genetics/isolation & purification

@article {pmid40332920,
year = {2025},
author = {Liu, H and Chen, W and Fang, X and Li, D and Xiong, Y and Xie, W and Chen, Q and You, Y and Lin, C and Wang, Z and Wang, J and Chen, D and Li, Y and Cai, P and Nie, C and Hong, Y},
title = {Impact of Ectropis grisescens Warren (Lepidoptera: Geometridae) Infestation on the Tea Plant Rhizosphere Microbiome and Its Potential for Enhanced Biocontrol and Plant Health Management.},
journal = {Insects},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/insects16040412},
pmid = {40332920},
issn = {2075-4450},
support = {2023XQ019//Key Technological Innovation and Industrialization Project/ ; 2022J011198//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01917//Project of Fujian Provincial Department of Science and Technology/ ; 2024J01916//Project of Fujian Provincial Natural Science Fund/ ; N2023Z007//Nanping Academy of Resource Industrialization Chemistry Project/ ; N2023J004//Key Project of the Nanping Natural Fund/ ; 202410397010//National College Student Innovation and Entrepreneurship Project/ ; },
abstract = {The root-associated microbiome significantly influences plant health and pest resistance, yet the temporal dynamics of its compositional and functional change in response to Ectropis grisescens Warren (Lepidoptera: Geometridae) infestation remain largely unexplored. The study took samples of leaves, roots, and rhizosphere soil at different times after the plants were attacked by E. grisescens. These samples were analyzed using transcriptomic and high-throughput sequencing of 16S rRNA techniques. The goal was to understand how the plant's defense mechanisms and the microbial community around the roots changed after the attack. Additionally, bacterial feedback assays were conducted to evaluate the effects of selected microbial strains on plant growth and pest defense responses. By conducting 16S rRNA sequencing on the collected soil samples, we found significant shifts in bacterial communities by the seventh day, suggesting a lag in community adaptation. Transcriptomic analysis revealed that E. grisescens attack induced reprogramming of the tea root transcriptome, upregulating genes related to defensive pathways such as phenylpropanoid and flavonoid biosynthesis. Metagenomic data indicated functional changes in the rhizosphere microbiome, with enrichment in genes linked to metabolic pathways and nitrogen cycling. Network analysis showed a reorganization of core microbial members, favoring nitrogen-fixing bacteria like Burkholderia species. Bacterial feedback assays confirmed that selected strains, notably Burkholderia cepacia strain ABC4 (T1) and a nine-strain consortium (T5), enhanced plant growth and defense responses, including elevated levels of flavonoids, polyphenols, caffeine, jasmonic acid, and increased peroxidase (POD) and superoxide dismutase (SOD) activities. This study emphasizes the potential of utilizing root-associated microbial communities for sustainable pest management in tea cultivation, thereby enhancing resilience in tea crops while maintaining ecosystem balance.},
}

@article {pmid40332703,
year = {2025},
author = {Lu, RL and Chen, YR and Yang, XF and Huang, XY and Liu, DZ and Hong, XP},
title = {Genetic liability to gut microbiota and inflammatory cytokines in relation to systemic lupus erythematosus risk: a multi-omics study.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40332703},
issn = {1434-9949},
support = {SZSM202111006//Sanming Project of Medicine in Shenzen Municipality/ ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) has been associated with gut microbiota in some studies. There is no clear evidence that cytokines act as mediators.

METHODS: We first assessed the differences in gut microbiota between SLE patients and healthy controls using 16S rDNA sequencing. Subsequently, we used the summary statistics of gut microbiota, cytokines, and SLE from large genome-wide association studies. To explore the causal relationships between gut microbiota and SLE and identify potential mediating cytokines, we performed bidirectional Mendelian randomization analyses. Finally, the levels of potentially mediating cytokines were determined by ELISA.

RESULTS: Fecal 16S rDNA sequencing showed that there was gut microbiota disorder in SLE patients. Based on two-sample analysis, seven gut microbiota taxa were causally associated with SLE. SLE influenced the relative abundance of two gut microbiota taxa in our large-scale MR study. Mediation analyses revealed that the causal relationship between genus Lachnospiraceae UCG001 and SLE was exclusively mediated by fibroblast growth factor 19 (FGF19) levels and the causal relationship between order Lactobacillales and SLE was exclusively mediated by tumor necrosis factor receptor superfamily member 9 (TNFRSF9) levels. Elevated levels of FGF19 affected the association between the reduced relative abundance of the genus Coprobacter and SLE, mediating by a proportion of 10.64% (P = 0.030). Furthermore, ELISA showed that circulating TNFRSF9 and FGF19 levels were higher in SLE patients than healthy controls.

CONCLUSION: Our study demonstrated that there is a causal link between some gut microbiota taxa and SLE. In addition, we revealed possible mediating effects in this relationship. Key Points • We first demonstrate a causal association between gut microbiota, cytokines, and SLE comprehensively. • Our experiments also confirmed that TNFRSF9 and FGF19 may play a role in SLE. These results provide new ideas for microbiome-based investigation of new mechanisms and therapies for SLE.},
}

@article {pmid40332367,
year = {2025},
author = {Ionescu, VA and Diaconu, CC and Gheorghe, G and Mihai, MM and Diaconu, CC and Bostan, M and Bleotu, C},
title = {Gut Microbiota and Colorectal Cancer: A Balance Between Risk and Protection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083733},
pmid = {40332367},
issn = {1422-0067},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/prevention & control/immunology/etiology ; *Gastrointestinal Microbiome ; Animals ; Risk Factors ; Probiotics ; },
abstract = {The gut microbiome, a complex community of microorganisms residing in the intestinal tract, plays a dual role in colorectal cancer (CRC) development, acting both as a contributing risk factor and as a protective element. This review explores the mechanisms by which gut microbiota contribute to CRC, emphasizing inflammation, oxidative stress, immune evasion, and the production of genotoxins and microbial metabolites. Fusobacterium nucleatum, Escherichia coli (pks+), and Bacteroides fragilis promote tumorigenesis by inducing chronic inflammation, generating reactive oxygen species, and producing virulence factors that damage host DNA. These microorganisms can also evade the antitumor immune response by suppressing cytotoxic T cell activity and increasing regulatory T cell populations. Additionally, microbial-derived metabolites such as secondary bile acids and trimethylamine-N-oxide (TMAO) have been linked to carcinogenic processes. Conversely, protective microbiota, including Lactobacillus, Bifidobacterium, and Faecalibacterium prausnitzii, contribute to intestinal homeostasis by producing short-chain fatty acids (SCFAs) like butyrate, which exhibit anti-inflammatory and anti-carcinogenic properties. These beneficial microbes enhance gut barrier integrity, modulate immune responses, and inhibit tumor cell proliferation. Understanding the dynamic interplay between pathogenic and protective microbiota is essential for developing microbiome-based interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, to prevent or treat CRC. Future research should focus on identifying microbial biomarkers for early CRC detection and exploring personalized microbiome-targeted therapies. A deeper understanding of host-microbiota interactions may lead to innovative strategies for CRC management and improved patient outcomes.},
}

Humans
*Colorectal Neoplasms/microbiology/prevention & control/immunology/etiology
*Gastrointestinal Microbiome
Animals
Risk Factors
Probiotics

@article {pmid40332366,
year = {2025},
author = {Liu, W and Wang, L and Ou, J and Peng, D and Zhang, Y and Chen, W and Wang, Y},
title = {Gut Microbiota Metabolites and Chronic Diseases: Interactions, Mechanisms, and Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083752},
pmid = {40332366},
issn = {1422-0067},
support = {82204748//the National Natural Science Foundation of China Youth Program [82204748]/ ; 82073923//the National Natural Science Foundation of China/ ; CACM-2022-QNRC2-B03//the Chinese Society of Traditional Chinese Medicine Young Talent Support Project Program/ ; [2023]No.85//the High-level Chinese Medicine Key Discipline Construction Project[National TCM Human Education Letter/ ; 202423l10050002//Science and Technology Innovation Tackling Plan Project of Anhui Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Chronic Disease/therapy ; Animals ; Cardiovascular Diseases/microbiology/metabolism ; Metabolic Diseases/microbiology/metabolism ; },
abstract = {The gut microbiota, shaped by factors such as diet, lifestyle, and genetics, plays a pivotal role in regulating host metabolism, immune function, and overall health. The diversity and balance of the gut microbiota are closely linked to the onset and progression of various chronic diseases. A growing body of evidence has demonstrated that alterations in the composition, function, and metabolites of the gut microbiota are significantly associated with cardiovascular diseases, including hypertension, atherosclerosis, and heart failure; metabolic disorders such as obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease; and gastrointestinal conditions like inflammatory bowel disease and colorectal cancer. Despite substantial advances in microbiome research, challenges remain in fully elucidating the causal relationships between the gut microbiota and disease, as well as in translating these insights into clinical applications. This review aims to investigate the regulatory pathways via which the gut microbiota affects cardiovascular health, metabolic function, and gastrointestinal disease. Additionally, it highlights emerging strategies for the prevention and treatment of these chronic conditions, focusing on microbiota-targeted therapies and personalized dietary interventions as promising approaches for improving health outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
Chronic Disease/therapy
Animals
Cardiovascular Diseases/microbiology/metabolism
Metabolic Diseases/microbiology/metabolism

@article {pmid40332266,
year = {2025},
author = {Aydin, M and Avci, GA and Yilmaz, UI and Avci, E},
title = {A new approach to osteoarthritis: gut microbiota.},
journal = {Revista da Associacao Medica Brasileira (1992)},
volume = {71},
number = {3},
pages = {e20241528},
doi = {10.1590/1806-9282.20241528},
pmid = {40332266},
issn = {1806-9282},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Osteoarthritis, Knee/microbiology ; Male ; Female ; Feces/microbiology ; Middle Aged ; Aged ; Case-Control Studies ; *Synovial Fluid/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Knee Joint/microbiology ; },
abstract = {OBJECTIVE: Studies investigating the relationship between the gut microbiome and osteoarthritis have increased in recent years. However, data on the relationship between joints and the gut microbiome are limited. The aim of this study was to determine whether there is a relation between knee joint fluid and gut microbiota in patients with knee osteoarthritis.

METHODS: This study included 40 individuals, 20 of whom were diagnosed with knee osteoarthritis and 20 of whom were considered healthy controls. Joint-fluid and stool samples were taken from the participants. Bacteria isolated from the samples were identified using a matrix-assisted laser desorption ionization-time of flight-mass spectrometry device.

RESULTS: Twenty-nine different bacteria were isolated from the stool samples and five bacteria were isolated from the joint-fluid samples. In our study, the same types of microorganisms (Enterococcus faecium and Staphylococcus hominis) were isolated from the stool and joint-fluid samples.

CONCLUSION: The data obtained in our study shed light on the uncertainty of how microorganisms, especially those identified in the knee and hip in the literature, reach these regions. The presence of intestinal bacteria in the knee joint fluid of osteoarthritis patients indicates that intestinal bacteria, especially in individuals with a weak immune system, malnutrition, and obesity, pass through the intestinal wall and reach other parts of the body via the bloodstream, a condition also known as "leaky gut."},
}

Humans
*Gastrointestinal Microbiome/physiology
*Osteoarthritis, Knee/microbiology
Male
Female
Feces/microbiology
Middle Aged
Aged
Case-Control Studies
*Synovial Fluid/microbiology
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
*Knee Joint/microbiology

@article {pmid40332187,
year = {2025},
author = {Lin, YR and Lam, LY and Chang, CM and Lam, HYP},
title = {Concomitant occurrence of chronic Schistosoma mansoni infection and chronic colitis restore immune imbalance and dysbiosis leading to protection against intestinal colitis and schistosome egg-induced intestinal fibrosis.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e240045},
doi = {10.1590/0074-02760240045},
pmid = {40332187},
issn = {1678-8060},
mesh = {Animals ; *Schistosomiasis mansoni/immunology/complications/pathology ; Chronic Disease ; *Colitis/immunology/parasitology/pathology ; *Dysbiosis/immunology/parasitology ; Disease Models, Animal ; Mice ; Fibrosis ; Enzyme-Linked Immunosorbent Assay ; Schistosoma mansoni/immunology ; Female ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: Schistosomiasis is one of the most devastating tropical diseases in developing countries and is usually misdiagnosed with colitis because the prevalence of co-occurrence of both diseases is high. Previously, infection of Schistosoma japonicum cercariae has been shown to provide immediate protection against dextran sodium sulphate (DSS)-induced acute colitis in mice models. Studies using synthesised peptides or soluble proteins from parasites also revealed similar protection against colitis. However, most of these studies were done within a short timeframe, which cannot completely represent the actual situation where natural infection of Schistosoma or colitis is usually chronic.

OBJECTIVES: This study aims to investigate how chronic schistosomiasis affects chronic intestinal inflammation.

METHODS: Mice were infected with Schistosoma mansoni and induced simultaneously with chronic colitis. The symptoms and severity of intestinal inflammation and fibrosis were investigated by disease activity index, histology, enzyme-linked immunosorbent assay (ELISA), and quantitative polymerase chain reaction (qPCR). Furthermore, immune analysis by ELISA and qPCR and microbiome analysis by 16S rDNA sequencing were done to investigate the underlying mechanism.

FINDINGS: Concomitant occurrence of chronic schistosomiasis and chronic colitis significantly alleviated colitis symptoms, lessened intestinal inflammation, and reduced egg-induced fibrosis. Further analysis revealed an alternation of the intestinal immunity and gut microbiome community in mice with both diseases, which could be the potential reason for this outcome.

MAIN CONCLUSIONS: Our results represent a mechanism of how schistosomiasis and chronic intestinal inflammation affect each other.},
}

Animals
*Schistosomiasis mansoni/immunology/complications/pathology
Chronic Disease
*Colitis/immunology/parasitology/pathology
*Dysbiosis/immunology/parasitology
Disease Models, Animal
Mice
Fibrosis
Enzyme-Linked Immunosorbent Assay
Schistosoma mansoni/immunology
Female
Gastrointestinal Microbiome
Male

@article {pmid40332099,
year = {2025},
author = {Wang, C and Li, Z and Huang, X and Xu, X and Xu, X and Zhang, K and Zhou, Y and Bai, J and Liu, Z and Jiang, Y and Tang, Y and Deng, X and Li, S and Hu, E and Peng, W and Xiong, L and Xiao, Q and Yang, Y and Qin, Q and Liu, S},
title = {Multi-Omic Analysis Reveals the Potential Anti-Disease Mechanism of Disease-Resistant Grass Carp.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083619},
pmid = {40332099},
issn = {1422-0067},
support = {2023YFD2401601//National Key Research and Development Program of China/ ; HARS-07//Earmarked Fund for HARS/ ; NSYYKY202305//Special Science Found of Nansha-South China Agricultural University Fishery Research Institute, Guangzhou/ ; 2023WK2001//Special Funds for the Construction of Innovative Province in Hunan/ ; CARS-45//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {Animals ; *Carps/microbiology/genetics/metabolism/immunology ; *Gastrointestinal Microbiome ; *Disease Resistance/genetics ; Liver/metabolism ; Male ; Transcriptome ; Female ; *Fish Diseases/microbiology/genetics/immunology ; Gene Expression Profiling ; Metabolomics/methods ; Multiomics ; },
abstract = {The gut-liver axis is essential in animal disease and health. However, the role of the gut-liver axis in the anti-disease mechanism of disease-resistant grass carp (DRGC) derived from the backcross of female gynogenetic grass carp (GGC) and male grass carp (GC) remains unclear. This study analyzed the changes in gut histopathology, fecal intestinal microflora and metabolites, and liver transcriptome between GC and DRGC. Histological analysis revealed significant differences in the gut between DRGC and GC. In addition, microbial community analyses indicated that hybridization induced gut microbiome variation by significantly increasing the proportion of Firmicutes and Bacteroidota in DRGC. Metabolomic data revealed that the hybridization-induced metabolic change was probably characterized by being related to taurocholate and sphinganine in DRGC. Transcriptome analysis suggested that the enhanced disease resistance of DRGC was primarily attributed to immune-related genes (SHMT2, GOT1, ACACA, DLAT, GPIA, TALDO1, G6PD, and FASN). Spearman's correlation analysis revealed a significant association between the gut microbiota, immune-related genes, and metabolites. Collectively, the gut-liver axis, through the interconnected microbiome-metabolite-gene pathway, may play a crucial role in the mechanism of greater disease resistance in DRGC, offering valuable insights for advancing the grass carp cultivation industry.},
}

Animals
*Carps/microbiology/genetics/metabolism/immunology
*Gastrointestinal Microbiome
*Disease Resistance/genetics
Liver/metabolism
Male
Transcriptome
Female
*Fish Diseases/microbiology/genetics/immunology
Gene Expression Profiling
Metabolomics/methods
Multiomics

@article {pmid40332093,
year = {2025},
author = {Ioannou, P and Katsoulieris, E and Afratis, NA},
title = {Matrix Dynamics and Microbiome Crosstalk: Matrix Metalloproteinases as Key Players in Disease and Therapy.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083621},
pmid = {40332093},
issn = {1422-0067},
support = {16378//Hellenic Foundation for Research and Innovation/ ; },
mesh = {Humans ; *Matrix Metalloproteinases/metabolism ; *Extracellular Matrix/metabolism ; Animals ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/metabolism ; *Microbiota ; },
abstract = {Matrix metalloproteinases (MMPs) are key enzymes involved in extracellular matrix (ECM) remodeling, regulating a wide range of cellular and immune processes in both homeostatic and pathological conditions. Host-microbiota interactions play a critical role in maintaining ECM balance; however, during dysbiosis, this regulation is disrupted, leading to compromised barrier integrity, pathogen translocation into circulation, and the development of systemic diseases and cancer. This review highlights the bidirectional relationship between MMP expression/activity and microbiota dysbiosis, emphasizing tissue-specific alterations in MMP activity that contribute to disease progression. In addition, it integrates interdisciplinary evidence to illustrate the MMP-dependent mechanisms underlying various pathologies associated with oral and gut microbiome dysbiosis, including long-range effects through the gut-skin and gut-brain axes. Thus, this review introduces the emerging field of MatrixBiome, which explores the complex interactions between the ECM, microbiota, and host tissues. Finally, it also outlines therapeutic strategies to modulate MMP levels, either indirectly through microbiome-targeted approaches (e.g., prebiotics, probiotics, and postbiotics) or directly using MMP inhibitors, offering promising avenues for future clinical interventions.},
}

Humans
*Matrix Metalloproteinases/metabolism
*Extracellular Matrix/metabolism
Animals
*Gastrointestinal Microbiome
Dysbiosis/microbiology/metabolism
*Microbiota

@article {pmid40331997,
year = {2025},
author = {Cucu, CI and Giurcăneanu, C and Poenaru, E and Popa, LG and Popa, MI and Chifiriuc, MC and Lazăr, V and Holban, AM and Gheorghe-Barbu, I and Muntean, AA and Caracoti, CȘ and Mihai, MM},
title = {Phenotypic and Genotypic Bacterial Virulence and Resistance Profiles in Hidradenitis Suppurativa.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083502},
pmid = {40331997},
issn = {1422-0067},
support = {PN-III-P1-1.1-PD-2019-1225//Unitatea Executiva Pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii/ ; },
mesh = {*Hidradenitis Suppurativa/microbiology ; Humans ; Virulence Factors/genetics/metabolism ; Virulence/genetics ; Biofilms/growth & development ; Phenotype ; Genotype ; *Drug Resistance, Bacterial/genetics ; Staphylococcus aureus/pathogenicity/genetics/drug effects ; Female ; Anti-Bacterial Agents/pharmacology ; Male ; Adult ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition, primarily affecting young individuals, with a significant impact on their quality of life due to recurrent, painful nodules, abscesses, and oozing sinus tracts, primarily affecting intertriginous areas. The pathogenesis of HS is multifactorial, involving a complex interplay between genetic predisposition, immune dysregulation, microbial, and environmental factors. While it is known that cutaneous and gut microbiome contribute to innate immune dysregulation in HS, their precise involvement in disease pathogenesis remains unclear. Despite several studies investigating the microbiome of HS lesions, either by culture-dependent or independent methods, there is no data available on the interplay between bacterial virulence profiles, clinical manifestations, and the host immune response. This study aimed to explore the phenotypic and genotypic resistance and virulence profiles of microorganisms isolated from HS lesions (including the expression of soluble virulence factors and the ability to develop biofilms), with a special focus on Staphylococcus aureus (S. aureus), one of the most frequent infectious agents of HS. A total of 92 bacterial strains, belonging to 20 different bacterial species, were isolated from the HS lesions of 23 patients. The strains of Staphylococcus, Corynebacterium, and Enterococcus expressed the highest levels of soluble virulence factors, such as hemolysins, lecithinase, and lipase, which are involved in bacterial persistence, local invasivity, and tissue damage. Moreover, a significant variation among bacterial species was noted regarding the capacity to develop biofilms, with a potential impact on disease chronicization, bacterial tolerance to antibiotics, and immune defense mechanisms. The genetic characterization of methicillin-resistant staphylococci revealed the presence of adhesins, hemolysin and enterotoxin genes as well as methicillin and macrolides resistance genes. Our findings highlight the critical role of virulence determinants, including bacterial biofilms, in HS pathogenesis, emphasizing the need for targeted therapeutic strategies to disrupt biofilms and mitigate infection severity.},
}

*Hidradenitis Suppurativa/microbiology
Humans
Virulence Factors/genetics/metabolism
Virulence/genetics
Biofilms/growth & development
Phenotype
Genotype
*Drug Resistance, Bacterial/genetics
Staphylococcus aureus/pathogenicity/genetics/drug effects
Female
Anti-Bacterial Agents/pharmacology
Male
Adult

@article {pmid40331988,
year = {2025},
author = {Gan, CM and Tang, T and Zhang, ZY and Li, M and Zhao, XQ and Li, SY and Yan, YW and Chen, MX and Zhou, X},
title = {Unraveling the Intricacies of Powdery Mildew: Insights into Colonization, Plant Defense Mechanisms, and Future Strategies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/ijms26083513},
pmid = {40331988},
issn = {1422-0067},
support = {2022YFD1700200//Moxian-Chen/ ; ZK[2023]-099//Moxian-Chen/ ; },
mesh = {*Plant Diseases/microbiology/immunology ; Disease Resistance/genetics ; Host-Pathogen Interactions ; *Ascomycota/pathogenicity ; Plant Immunity ; Gene Expression Regulation, Plant ; *Plants/microbiology/immunology ; *Erysiphe/pathogenicity ; },
abstract = {Powdery mildew, a debilitating phytopathogen caused by biotrophic fungi within the order Erysiphales, endangers crop yields and global food security. Although traditional approaches have largely emphasized resistant cultivar development and chemical control, novel strategies are necessary to counter the advent of challenges, such as pathogen adaptation and climate change. This review fully discusses three principal areas of pathogen effector functions, e.g., the reactive oxygen species (ROS)-suppressive activity of CSEP087, and host susceptibility factors, like vesicle trafficking regulated by Mildew Locus O (MLO). It also briefly mentions the transcriptional regulation of resistance genes mediated by factors, like WRKY75 and NAC transcription factors, and post-transcriptional regulation via alternative splicing (As). In addition, this discussion discusses the intricate interactions among powdery mildew, host plants, and symbiotic microbiomes thereof, highlighting the mechanism through which powdery mildew infections disrupt the foliar microbiota balance. Lastly, we present a new biocontrol approach that entails synergistic microbial consortia, such as combinations of Bacillus and Trichoderma, to induce plant immunity while minimizing fungicide dependency. Through the study of combining knowledge of molecular pathogenesis with ecological resilience, this research offers useful insights towards climate-smart crop development and sustainable disease-management strategies in the context of microbiome engineering.},
}

*Plant Diseases/microbiology/immunology
Disease Resistance/genetics
Host-Pathogen Interactions
*Ascomycota/pathogenicity
Plant Immunity
Gene Expression Regulation, Plant
*Plants/microbiology/immunology
*Erysiphe/pathogenicity

@article {pmid40331253,
year = {2025},
author = {Bai, J and Zhao, Y and Wang, Z and Qin, P and Huang, J and Cheng, Y and Wang, C and Chen, Y and Liu, L and Zhang, Y and Wu, B},
title = {Stroke-Associated Pneumonia and the Brain-Gut-Lung Axis: A Systematic Literature Review.},
journal = {The neurologist},
volume = {},
number = {},
pages = {},
doi = {10.1097/NRL.0000000000000626},
pmid = {40331253},
issn = {2331-2637},
abstract = {BACKGROUND: Stroke-associated pneumonia (SAP), a highly lethal complication following stroke, is closely linked to dysregulation of the "brain-gut-lung axis." Accumulating evidence indicates that stroke triggers intestinal alterations through the brain-gut axis, while multiple studies confirm that gut-derived changes can mediate pneumonia through the gut-lung axis. However, the mechanisms connecting stroke-induced intestinal dyshomeostasis to SAP remain incompletely elucidated, and the multiorgan interaction mechanisms of the "brain-gut-lung axis" in SAP pathogenesis require further exploration.

REVIEW SUMMARY: This systematic literature review systematically searched databases, including PubMed, using the keywords "stroke," "gastrointestinal microbiome," and "bacterial pneumonia," incorporating 80 mechanistic studies. Key findings reveal that stroke initiates a cascade of "neuro-microbial-immune" pathway interactions along the brain-gut-lung axis, leading to intestinal dyshomeostasis characterized by microbiota and metabolite alterations, barrier disruption, immune dysregulation, inflammatory responses, and impaired gut motility. These intestinal perturbations ultimately disrupt pulmonary immune homeostasis, promoting SAP development. In addition, stroke directly induces vagus nerve injury through the brain-gut axis, resulting in impaired swallowing and cough reflexes that exacerbate aspiration-related pulmonary infection risks.

CONCLUSIONS: Elucidating the role of the brain-gut-lung axis in SAP pathogenesis provides critical insights into its underlying mechanisms. This paradigm highlights intestinal homeostasis modulation and vagus nerve stimulation as promising therapeutic strategies for SAP prevention and management, advancing a multitargeted approach to mitigate poststroke complications.},
}

@article {pmid40331250,
year = {2025},
author = {Sugden, S and Serrouya, R and Neufeld, L and Schwantje, H and St Clair, CC and Stein, L and Spribille, T},
title = {Endangered Deep-Snow Mountain Caribou Have a Distinct Winter Diet and Gut Microbiome That May Be Altered by Maternal Penning.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17783},
doi = {10.1111/mec.17783},
pmid = {40331250},
issn = {1365-294X},
support = {RGPIN-2019-04399//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2019-04892//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2023-04892//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Understanding species- or population-specific dietary specialisation is key to informing habitat conservation needs and successful ex situ recovery programs for many endangered species. One of the most endangered populations in Canada, the behaviourally distinct deep-snow ecotype of the Southern Mountain caribou, is characterised by a winter diet of arboreal rather than terrestrial lichens. We hypothesised that this dietary variation would produce a distinct gut microbiome in deep-snow mountain caribou relative to their shallow-snow counterparts. We additionally hypothesised that the temporary alteration of natural diets for ex situ conservation programs, including the provision of commercial pelleted feed and volunteer-collected lichens during maternity penning of pregnant cows, may alter this specialised microbiome. Here, we use faecal DNA metabarcoding to compare diet and gut microbiome composition among various herds of deep- and shallow-snow caribou, captive deep-snow caribou from the Revelstoke maternity pen, and semi-domesticated reindeer. Our results confirm that free-ranging deep-snow caribou specialise on the arboreal hair lichens Bryoria and Nodobryoria, and we show that this correlates with a microbiome distinct from that of shallow-snow caribou specialising on the terrestrial lichens Cladonia and Stereocaulon. We also show that maternity penning of deep-snow caribou significantly altered forage consumption and microbiome composition: penned caribou consumed more foliose lichens and had a distinct microbiome compared to free-ranging caribou. Our results suggest that managers should carefully consider the preferred forage of caribou populations when designing interventions that require diet modification. We further suggest that faecal samples of caribou and other dietary specialists be routinely monitored for diet and microbiome composition, especially during periods of captivity or diet modification, as an additional component of conservation assessments.},
}

@article {pmid40331220,
year = {2025},
author = {Wang, Y and Wei, C and Chen, Z and Zhou, M and Huang, L and Chen, C},
title = {Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1582122},
pmid = {40331220},
issn = {2297-1769},
abstract = {Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.},
}

@article {pmid40331097,
year = {2025},
author = {Leonardo, J and Hertanto, R and Surya, R and Syahputra, RA and Humayrah, W and Sabrina, N and Taslim, NA and Tallei, TE and Tjandrawinata, RR and Nurkolis, F},
title = {Delites™ supplementation prevents metabolic syndrome onset and modulates gut microbiome in male Sprague Dawley rats fed on cholesterol- and fat-enriched diet: a randomized preclinical trial study.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1571473},
pmid = {40331097},
issn = {2296-861X},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is a global health concern, characterized by a combination of dyslipidemia, insulin resistance, obesity, and hypertension, significantly increasing the risk of type 2 diabetes mellitus (T2DM) and cardiovascular diseases. Gut microbiota plays a pivotal role in MetS pathophysiology, with dysbiosis exacerbating metabolic impairments. Delites™, a supplement inspired by Traditional Chinese Medicine, has shown potential in modulating gut microbiota and mitigating MetS.

OBJECTIVES: This study aimed to evaluate the effects of Delites™ supplementation on metabolic health and gut microbiota composition in male Sprague Dawley rats fed a cholesterol- and fat-enriched diet (CFED).

METHODS: A randomized preclinical trial was conducted on 32 rats divided into four groups: control-normal, CFED, CFED+low-dose Delites™ (54 mg/kg), and CFED+high-dose Delites™ (108 mg/kg). Parameters including lipid profiles, enzymatic activity, molecular biomarkers, and gut microbiota composition were analyzed.

RESULTS: Delites™ significantly improved lipid profiles, reduced inflammation (TNF-α), enhanced anti-inflammatory markers (IL-10), and increased energy metabolism regulator PGC-1α. Gut microbiota modulation showed increased beneficial genera (Bifidobacterium, Lactobacillus) and reduced pathogenic Proteus, improving microbial diversity.

CONCLUSION: Delites™ supplementation effectively mitigates MetS through metabolic and microbiota modulation. These findings highlight its potential for precision medicine approaches to combat metabolic disorders. Further research is needed to explore its long-term effects and translational relevance in humans.},
}

@article {pmid40331023,
year = {2025},
author = {Bachtiar, BM and Tahapary, DL and Fath, T and Theodorea, CF and Haerani, N and Soeroso, Y and Shahab, SN and Wildan, A and Runtu, FMJG and Tadjoedin, FM and Ayuningtyas, D and Amir, L and Bachtiar, EW},
title = {Saccharibacteria (TM7) in saliva and subgingival microbiome as a predictor for gingivitis in individuals with type2 diabetes evaluated by qPCR.},
journal = {Frontiers in dental medicine},
volume = {6},
number = {},
pages = {1550936},
pmid = {40331023},
issn = {2673-4915},
abstract = {Oral samples are widely used for studying oral microbiome in health and diseases. In this study, saliva and subgingival biofilm (SGB) samples obtained from patients with type2 diabetes (T2DM), without periodontitis (G1 group), with gingivitis (G2 group), and periodontitis (G3 group), were used to compare the abundance of Saccharibacteria (TM7), its host's bacteria (Schaalia odontolytica), periodontopathogen (Represented by Fusobacterium nucleatum), and nitrate-reducing bacteria (represented by Rothia mucilaginosa). The gingival crevicular fluid were also used to analyze the transcription levels of interleukin-6 (IL-6) and C-reactive protein (CRP). Healthy individuals' oral samples served as a control, and the targeted bacteria and inflammatory indicators were detected and measured using real-time PCR. The results showed that in either sample, the abundance of TM7 and other targeted bacteria showed a similar profile. Notably, within participants with T2DM, the abundance of TM7 was similar in G1 and G2 groups, but significantly decreased in G3 group. With the exception of the SGB of the G3 group, the relationship between TM7 and its bacterial host was strongly positive across all evaluated samples. Furthermore, CRP had higher transcription levels than IL-6 across the entire group. Despite the fact that the G3 group showed an adverse relationship between TM7 and CRP, patients with T2DM generally showed a positive correlation between TM7 and IL-6/CRP, which was verified by a receiver operating curve.},
}

@article {pmid40330867,
year = {2025},
author = {Zhu, Y and Zeng, X and Zhang, A and Lu, B and Wu, M and Liu, H and Zhu, F and Lin, R},
title = {Correlation of tongue coating thickness with microinflammatory state and oral microbiome in maintenance hemodialysis patients.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2488054},
pmid = {40330867},
issn = {2000-2297},
abstract = {AIM: This study investigated the correlation between tongue coating thickness (TCT), micro-inflammatory state (MIS), and oral microbiome in maintenance hemodialysis (MHD) patients.

METHODS: Forty MHD patients (20 thin-tongue coating [BTZ], 20 thick-tongue coating [HTZ]) and 15 healthy controls (DZZ) were enrolled. Blood microinflammatory markers were analyzed in all patients. Saliva samples from 15 HTZ, 15 BTZ, and 15 DZZ underwent 16S rRNA sequencing.

RESULTS: HTZ patients exhibited higher microinflammatory marker levels than BTZ. Oral microbiome species richness in DZZ surpassed that of the MHD groups, with distinct structural differences, particularly between HTZ and DZZ. HTZ showed higher abundances of Actinobacillus, Peptostreptococcus, and Lachnospiraceae NK4A136 group than BTZ. Correlation analysis revealed a positive correlation between the levels of IL-6 and TNF-α and the abundance of Fusobacterium, but a negative correlation with Streptococcus. Additionally, the TNF-α level positively correlated with Campylobacter.

CONCLUSION: Thick tongue coating in MHD patients is associated with elevated microinflammation and altered oral microbiome, suggesting a link between inflammation and microbial dysbiosis.},
}

@article {pmid40330818,
year = {2025},
author = {Chen, M and Huang, K and Luo, W and Zhang, F and Gan, H and Yang, Z},
title = {Hyodeoxycholic Acid Ameliorates Metabolic Syndrome Through Pathways of Primary Bile Acid Synthesis and Fatty Acid Degradation: Insights From a Rat Model.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {3611-3630},
pmid = {40330818},
issn = {1177-8881},
mesh = {Animals ; Rats ; *Bile Acids and Salts/biosynthesis/metabolism ; *Metabolic Syndrome/drug therapy/metabolism ; Male ; *Fatty Acids/metabolism ; Disease Models, Animal ; *Deoxycholic Acid/pharmacology/analogs & derivatives/administration & dosage ; Rats, Sprague-Dawley ; Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Bile acids (BAs) play a crucial role in metabolic regulation, but their specific functions in metabolic syndrome (MS) remain unclear. Hyodeoxycholic acid (HDCA) has shown potential effects in non-alcoholic fatty liver disease (NAFLD), yet its role in MS is unexplored.

AIM: This study aims to assess whether HDCA is a characteristic BA of MS and to investigate its intervention effects and potential mechanisms.

METHODS: We employed 16S rDNA sequencing and UHPLC-MS/MS to investigate the dynamics of the gut microbiota and BA profiles in rats and conducted a correlation study between indices, identifying HDCA as the potential characteristic BA. We then examined its interventional effects in MS rats comparing efficacy with the positive drug of MS (metformin). Subsequently, liver RNA sequencing (RNA-seq), gene set enrichment analysis (GSEA), and Wes Automated Simple Western assays were employed to investigate mechanisms of HDCA ameliorating MS.

RESULTS:  HDCA was identified as a characteristic BA for MS, exhibiting a significant positive correlation with beneficial gut bacteria and a negative correlation with harmful bacteria, and highly inversely related to various abnormal MS indexes. HDCA treatment led to significant improvements in metabolic abnormalities in MS rats, with a central role in altering serum BA profiles and profoundly modifying the gut microbiome composition. The results of RNA-seq and GSEA indicated that HDCA influenced the expression of genes related to primary bile acid synthesis and fatty acid degradation (p<0.05). Wes assays validated that FXR, CYP7A1, CYP7B1, PPARα, CPT1, CPT2, FABP1, HMGCS1 and HMGCS2 proteins in MS rats exhibited significant changes after HDCA treatment (p<0.05), and this was more effective than metformin treatment.

CONCLUSION: These study is the first to highlight HDCA as a therapeutic candidate for MS and provides new insights into the BA-MS axis, though further validation is needed.},
}

Animals
Rats
*Bile Acids and Salts/biosynthesis/metabolism
*Metabolic Syndrome/drug therapy/metabolism
Male
*Fatty Acids/metabolism
Disease Models, Animal
*Deoxycholic Acid/pharmacology/analogs & derivatives/administration & dosage
Rats, Sprague-Dawley
Gastrointestinal Microbiome/drug effects

@article {pmid40330725,
year = {2025},
author = {Gong, D and Gao, Y and Shi, R and Xu, X and Yu, M and Zhang, S and Wang, L and Dong, Q},
title = {Corrigendum: The gastric microbiome altered by A4GNT deficiency in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1604379},
doi = {10.3389/fmicb.2025.1604379},
pmid = {40330725},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1541800.].},
}

@article {pmid40330693,
year = {2025},
author = {Abbasi, E},
title = {Climate Change and Vector-Borne Disease Transmission: The Role of Insect Behavioral and Physiological Adaptations.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {7},
number = {1},
pages = {obaf011},
pmid = {40330693},
issn = {2517-4843},
abstract = {Climate change is profoundly reshaping the behavior, physiology, and distribution of insect vectors, with significant implications for vector-borne disease transmission. Rising temperatures, shifting precipitation patterns, and extreme weather events are driving behavioral adaptations such as altered host-seeking patterns, modified resting site preferences, and extended seasonal activity. Concurrently, vectors exhibit physiological plasticity, including enhanced thermal tolerance, desiccation resistance, and accelerated reproductive cycles, which contribute to increased survival and vector competence. This review synthesizes current research on climate-driven adaptations in major disease vectors, focusing on their epidemiological consequences and implications for public health interventions. A systematic literature review was conducted using major scientific databases to assess the impact of climate change on insect vector adaptation. Studies examining temperature-induced behavioral shifts, physiological modifications, and changes in vector competence were analyzed to identify emerging trends and knowledge gaps. Findings indicate that climate-driven vector adaptations are increasing the efficiency of disease transmission, enabling the geographic expansion of vector populations and prolonging transmission seasons. These changes challenge existing vector control strategies, necessitating innovative approaches such as genetic engineering, microbiome-based interventions, and climate-informed surveillance systems. Given the accelerating impact of climate change, there is an urgent need for adaptive, evidence-based control strategies to mitigate the growing threat of vector-borne diseases and enhance global health resilience.},
}

@article {pmid40330104,
year = {2025},
author = {Molloy, MM and McLennan, EA and Fox, S and Belov, K and Hogg, CJ},
title = {Range-Wide Assessment of the Tasmanian Devil Gut Microbiome.},
journal = {Ecology and evolution},
volume = {15},
number = {5},
pages = {e71196},
pmid = {40330104},
issn = {2045-7758},
abstract = {The gut microbiome is an important component of host health and function and is influenced by internal and external factors such as host phylogeny, age, diet, and environment. Monitoring the gut microbiome has become an increasingly important management tool for wild populations of threatened species. The Tasmanian devil (Sarcophilus harrisii) is the largest extant carnivorous marsupial from the island state of Tasmania, Australia. Devils are currently endangered due to devil facial tumor disease. Previous assessments have shown differences between captive and wild devil gut microbiomes and changes during translocations. However, wild gut microbiome variability across Tasmania and the drivers of these differences are not well understood. We conducted a range-wide assessment of gut microbiomes at 10 locations across Tasmania, via 16S rRNA sequencing, and tested the influence of diet (12S vertebrate sequencing), location, sex, and cohort. We show that the five most abundant phyla and genera were consistent across all 10 locations. Location, cohort, and sex impacted bacterial richness, but location did not impact diversity. While there were differences in diet across the state, there was no strong evidence of differences between juveniles and adults, nor between males and females. Contrary to our hypothesis, the vertebrate diet explained a small amount of variation in microbial communities. We suspect that other variables, such as environmental factors and immune system development, may have a stronger influence on gut microbiome variability. Dietary components missed by our 12S primer, including invertebrates and plants, may also contribute to these patterns. Adjustments to dietary supplementation are not recommended when preparing devils for translocation to different sites. Future research should prioritize collecting environmental samples for microbial analysis and integrating metabolomics to elucidate functional differences associated with Tasmanian devil gut microbiome variability.},
}

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

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

@article {pmid40330019,
year = {2025},
author = {Fang, P and Wen, Y and Deng, W and Liang, R and He, P and Wang, C and Fan, N and Huo, K and Zhao, K and Li, C and Bai, Y and Ma, Y and Hu, L and Guan, Y and Yang, S},
title = {Investigation of dynamic microbial migration patterns in the respiratory tract.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1542562},
pmid = {40330019},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; Prospective Studies ; Male ; Female ; Middle Aged ; *Microbiota ; Sputum/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Respiratory System/microbiology ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Oropharynx/microbiology ; Bayes Theorem ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The role of the respiratory microbiome in lung diseases is increasingly recognized, with the potential migration of respiratory pathogens being a significant clinical consideration. Despite its importance, evidence elucidating this phenomenon remains scarce.

METHODS: This prospective study collected clinical samples from patients with suspected lower respiratory tract infections (LRTI), including oropharyngeal swabs (OPS), sputum, and bronchoalveolar lavage fluid (BALF). Metagenomic next-generation sequencing (mNGS) was employed to analyze respiratory microbial diversity, complemented by Bayesian source tracking and sequence alignment analyses to explore pathogen migration patterns.

RESULTS: A cohort of 68 patients was enrolled, with 56 diagnosed with LRTI and 12 with non-infectious respiratory conditions. A statistically significant disparity in respiratory microbiome diversity was observed between infected and non-infected groups (p < 0.05). Intriguingly, no significant variations in microbial community structure, including alpha and beta diversity, were detected across different respiratory tract sites within individuals. The Bayesian source tracking analysis revealed a pronounced migration pattern among pathogens compared to the overall microbial community, with migration ratios of 51.54% and 1.92%, respectively (p < 0.05). Sequence similarity analysis further corroborated these findings, highlighting a notable homology among specific migrating pathogens.

CONCLUSION: This study represents a pioneering effort in deducing pathogen migration patterns through microbial source tracking analysis. The findings provide novel insights that could significantly advance clinical diagnostics and therapeutic strategies for respiratory infections.},
}

Humans
*Respiratory Tract Infections/microbiology
Prospective Studies
Male
Female
Middle Aged
*Microbiota
Sputum/microbiology
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Respiratory System/microbiology
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Oropharynx/microbiology
Bayes Theorem
*Bacteria/classification/genetics/isolation & purification

@article {pmid40330018,
year = {2025},
author = {Zhou, P and Liu, Q and Zhao, Y and Wu, Y and Shen, J and Duan, T and Che, L and Zhang, Y and Yan, H},
title = {Yeast protein as a fishmeal substitute: impacts on reproductive performance, immune responses, and gut microbiota in two sow hybrids.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1579950},
pmid = {40330018},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Swine ; Female ; *Reproduction/drug effects ; *Animal Feed/analysis ; Dietary Supplements ; Pregnancy ; *Fungal Proteins/administration & dosage ; Diet ; Breeding ; },
abstract = {INTRODUCTION: The persistent African swine fever epidemic has significantly compromised China's swine production. To accelerate production recovery, commercial farms are increasingly adopting retention of two-way backcross sows (Landrace × Yorkshire × Landrace, LLY) for breeding. This study aimed to investigate the effects of yeast protein, an emerging sustainable protein source, on reproductive performance, immune responses, and gut microbiota in two-way crossbred sows (Landrace × Yorkshire, LY) and LLY sows.

METHODS: The experiment employed a 2×2 factorial design evaluating two fixed factors: sow hybrid (LY vs LLY) and yeast protein supplementation (0% vs 2.6%). The four treatment groups were: LY sows without yeast protein supplementation (LY-C), LLY sows without yeast protein supplementation (LLY-C), LY sows with yeast protein supplementation (LY-YP), and LLY sows with yeast protein supplementation (LLY-YP). A total of one hundred healthy sows of 2-6 parities (50 LY sows and 50 LLY sows), were stratified by backfat thickness, body weight, and parity, then randomly allocated to the four treatment groups on day 105 of gestation, with 25 sows in each group. The experimental period lasted from day 106 of gestation to day 18 of lactation.

RESULTS AND CONCLUSION: Yeast protein supplementation showed no significant effects on most reproductive parameters of different sow hybrids, but reduced backfat loss by 30.5% during lactation (P < 0.05) and demonstrated a numerical reduction in mummification rate of fetuses (P = 0.06). Immunological assessments revealed that LLY sows exhibited 26.8% lower serum IgM concentration than LY sows (P < 0.05), while yeast protein supplementation significantly reduced serum IL-1β levels by 45.6% (P < 0.05) on day 18 of lactation. 16S rRNA gene sequencing analysis revealed comparable fecal microbial diversity across treatments (P > 0.05), though differences were observed in certain bacterial genera between LY and LLY sows during late gestation and lactation. Yeast protein supplementation enriched beneficial bacteria including Ruminococcaceae_UCG-002, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R_7_group, while suppressing potentially detrimental bacteria such as Family_XIII_AD3011_group (P < 0.05). These findings demonstrate the practical feasibility of retaining LLY sows for commercial breeding. Yeast protein supplementation, as a substitute for fishmeal during late gestation and lactation, significantly reduced lactational backfat loss, moderately attenuated inflammatory response, and enhanced gut microbiome homeostasis through selective microbial enrichment in sows.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Swine
Female
*Reproduction/drug effects
*Animal Feed/analysis
Dietary Supplements
Pregnancy
*Fungal Proteins/administration & dosage
Diet
Breeding

@article {pmid40329984,
year = {2025},
author = {Tighe, SW and Vellone, DL and Tracy, KM and Lynch, DB and Finstad, KH and Mcllelan, MC and Dragon, JA},
title = {Microbiome and Microbial Profiling of Arctic Snow Using Whole Genome Sequencing, Psychrophilic Culturing, and Novel Sampling Techniques.},
journal = {Journal of biomolecular techniques : JBT},
volume = {36},
number = {1},
pages = {},
pmid = {40329984},
issn = {1943-4731},
mesh = {*Microbiota/genetics ; Arctic Regions ; *Whole Genome Sequencing/methods ; *Snow/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Fungi/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {Recent advances in massively parallel DNA sequencing have enabled researchers to study new areas of extreme environments. Of particular interest to many researchers are areas of the Arctic that have yet to be comprehensively examined using DNA techniques. These modern approaches to microbial profiling provide new critical data on systems biology not yet seen before from Arctic samples. The discovery of new microbes, microbial biochemical pathways, and biosynthetic gene clusters are critically important when characterizing the Arctic snow microbiome and can provide insights to discovering valuable biosynthetic gene clusters. In this study, 2 L of snow was collected from 15 sites 12 km east outside of Ilulissat, Greenland, using DNA-free sterile techniques. Snow was allowed to melt and immediately concentrated using the InnovaPrep CP sample concentrator. Whole genome DNA sequencing was performed on extracts using both Illumina and Nanopore sequencing as well as psychrophilic culturing. Individual cultures were also sequenced to determine whole genome content and species identity. The results showed a wide-ranging microbiome across the snow fields, including bacteria, yeast, and fungi, with Granulicella, Methylobabcterium, Nostoc, Sphingomonas, and Streptomyces being consistently detected at higher levels across the majority of sites and sequencing platforms, while Belnapia, Chlorogloea, Hymenobacter, Mesorhizobium, Narcardioides, Pseudomonas, Pseudonocardia, Roseomonas, and Solirubrobacter at comparatively lower abundances. The results of culture data for snow sites reveal Pseudomanas sp., Pseudomonas fluorescens Group, unknown Microbacteriaceae sp., Variovorax sp., Robbsia andropogonis, and low concentrations of Aureobasidium sp., Stylodothis sp., Sphingomonas sp., Hymenobacter sp., Caballeronia sordidicola, and two unknown species of yeast and one unknown species of bacteria.},
}

*Microbiota/genetics
Arctic Regions
*Whole Genome Sequencing/methods
*Snow/microbiology
*Bacteria/genetics/classification/isolation & purification
Fungi/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
Phylogeny

@article {pmid40329957,
year = {2025},
author = {Yamamoto, K},
title = {Revisiting the Etiology and Management of Atopic Dermatitis: A Perspective on Skin Microbiota, Bathing Habits, and Surfactant-Free Skincare.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {18},
number = {},
pages = {1087-1093},
pmid = {40329957},
issn = {1178-7015},
abstract = {The current consensus on the pathophysiology of atopic dermatitis (AD) involves Th2/Th22 inflammation, genetic predisposition such as filaggrin mutations, and skin barrier dysfunction. Meanwhile, AD has been hypothesized to be primarily caused by the defective formation of the commensal microbial community with insufficient skin regeneration as a secondary aggravating factor. AD presents with itchy, red, swollen, and cracked skin. Conventional treatments include emollients, topical corticosteroids, calcineurin inhibitors, and newer biologics. In Japan, moist wound healing techniques that promote autologous tissue regeneration have shown promising results, which have led to the development of novel, surfactant-free moisturizers designed to combat skin dryness. Based on these findings, this perspective proposes a new etiology of AD and considers suitable countermeasures. Recommendations include limiting newborn bathing to three times per week, discontinuing soap and shampoo applications, and using bathing additives containing petroleum jelly to neutralize the residual chlorine in tap water. Cognitive behavioral therapy strategies that substitute scratching with moisturizer application are also recommended. Additional measures, including smoking cessation by both patients and family members, and stress management, may reduce disease severity. This perspective article outlines hypotheses rather than established evidence. Some suggestions (eg, bathing frequency) are based on clinical experience or emerging findings that require further study.},
}

@article {pmid40329860,
year = {2025},
author = {Li, W and Marx, N and Yang, Q and Fang, D and Zhang, Y},
title = {Obesity: Next game changer of allergic airway diseases?.},
journal = {Clinical and translational medicine},
volume = {15},
number = {5},
pages = {e70316},
doi = {10.1002/ctm2.70316},
pmid = {40329860},
issn = {2001-1326},
support = {82371121//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 82271148//National Natural Science Foundation of China/ ; U20A20399//National Natural Science Foundation of China/ ; 2024A1515010052//Natural Science Foundation of Guangdong Province/ ; 2022A1515011787//Natural Science Foundation of Guangdong Province/ ; 2024A04J6570//Science and Technology Program of Guangzhou/ ; 2023A03J0209//Science and Technology Program of Guangzhou/ ; 0920220214//the Guangdong Provincial Pearl River Talents Program/ ; },
mesh = {Humans ; *Obesity/complications/epidemiology/therapy ; Asthma/epidemiology ; Prevalence ; *Hypersensitivity/epidemiology ; },
abstract = {Obesity and allergic diseases are global health concerns, both of which are seeing an increase in prevalence in recent years. Obesity has been recognised as an important comorbidity in subpopulations with allergic airway diseases, which represents a unique phenotype and endotype. Obesity-related allergic airway diseases are associated with exacerbated clinical symptom burden, altered immune response, increased disease severity and compromised predictive capability of conventional biomarkers for evaluating endotype and prognosis. Moreover, treatment of obesity-related allergic airway diseases is challenging because this unique endotype and phenotype is associated with poor response to standard therapeutic strategies. Therapeutic regimen that involves weight loss by non-surgical and surgical interventions, gut microbiome-targeted treatment, glucagon-like peptide-1 receptor agonist and other agents should be considered in this population. In this review, we outline the current knowledge of the impact of obesity on prevalence, endotypes, clinical symptom and management of allergic airway diseases. Increased understanding of the implications of obesity may contribute to better treatment options for the obesity-related refractory airway inflammation, particularly in precision medicine. KEY POINTS: Obesity can increase the prevalence of allergic airway diseases such as asthma, AR, and CRSwNP. Obesity alters the immune endotype and exacerbates clinical symptoms of respiratory allergic diseases. Obesity-related allergic airway diseases exhibit therapeutic resistance to standard treatment. Obesity-related allergic airway diseases constitute a distinct category of endotypes and phenotypes, requiring further in-depth research and novel therapeutic approaches.},
}

Humans
*Obesity/complications/epidemiology/therapy
Asthma/epidemiology
Prevalence
*Hypersensitivity/epidemiology

@article {pmid40329736,
year = {2025},
author = {Chandrasekaran, S and Rao, SS and Shetty, V},
title = {Association Between Oral Microbiome in Children Undergoing Palatoplasty and Surgical Site Infection.},
journal = {The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association},
volume = {},
number = {},
pages = {10556656251335181},
doi = {10.1177/10556656251335181},
pmid = {40329736},
issn = {1545-1569},
abstract = {ObjectiveTo determine the prevalent preoperative oral microbial flora in children undergoing palatoplasty and its association with surgical site infection (SSI).DesignProspective observational longitudinal study.SettingSingle-center study done at tertiary care institute of Craniofacial surgery during the period of October 2022 to April 2024.ParticipantsThe study participants were the children posted for palatoplasty in our institution. Children with other major anomalies, immunodeficiency, and systemic illness were excluded. A total of 30 consecutive samples were enrolled during the study period, and all were followed up to finish the study.InterventionsSubgingival plaque samples were taken preoperatively and one postoperatively in the event of SSI and culture sensitivity analysis was done to detect pathogenic micro-organisms.Outcome measuresRisk analysis done for the baseline characteristics.ResultsMost common pathogenic organism seen preoperatively was Streptococcus mitis (34.8%) followed by Klebsiella pneumoniae (26%) and Staphylococcus aureus (26%). Bottle-fed children and those with preoperative infections had an adjusted odds ratio of 36.56 (P = .004) and 5.71 (P = .05), respectively, for colonization by pathogenic flora. The incidence of SSI was 25.8% in the population, with K pneumoniae as the most common cause (75%). The children who were underweight and had past hospital admission had an odds ratio of 16.67 (P = .002) and 10.2 (P = .009) for developing SSI.ConclusionWe conclude that bottle feeding and past infections play a role in colonization by pathogenic flora. Klebsiella pneumoniae is the common organism causing SSI, and nutrition status plays a role in development of SSI.},
}

@article {pmid40329613,
year = {2025},
author = {Ajith, TA and Anita, B},
title = {Impact of Gut Microbiota and Probiotics on Rheumatoid Arthritis: A Potential Treatment Challenge.},
journal = {International journal of rheumatic diseases},
volume = {28},
number = {5},
pages = {e70266},
doi = {10.1111/1756-185X.70266},
pmid = {40329613},
issn = {1756-185X},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/therapeutic use/adverse effects ; *Arthritis, Rheumatoid/microbiology/immunology/therapy/diagnosis ; Dysbiosis ; Treatment Outcome ; *Bacteria/immunology/growth & development/metabolism ; Animals ; *Intestines/microbiology/immunology ; Host-Pathogen Interactions ; },
abstract = {Over the past few decades, there has been a surge in global study on the relationship between gut microbiota and human health. Numerous human illnesses have been linked to dysbiosis. Gram-positive firmicutes and Gram-negative bacteroidetes are the two leading bacterial phyla that make up 90% of the gut microbiome. Many symbionts in the gut environment establish intricate relationships with host defense to stop both local and non-native dangerous bacteria from colonizing and invading. Dysbiosis alters the paracellular route and damages the epithelium, enabling them to penetrate the epithelium and come into contact with the immune cells. Impaired intestinal barrier function, immune regulation mediated by metabolites derived from the gut microbiota, posttranslational modification of host proteins such as increased citrullination, regulation of the gut microbiota's effect on immune cells, intestinal epithelial cell autophagy, interaction between the microbiome and human leukocyte antigen alleles, and interaction with microRNAs are some of the mechanisms involved in rheumatoid arthritis (RA). The gut microbiota, Prevotella copri, and Collinsella spp. were shown to be higher in the early/preclinical phases of RA, while Bacteroidetes, Bifidobacteria, and Eubacterium rectale were found to be lower. Probiotic-based early dietary intervention may reduce inflammation and slow the rate of joint deterioration, and such intervention can also aid in the restoration of gut microbiota equilibrium. This review article describes the gut microbial dysbiosis and role of probiotics in RA.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Probiotics/therapeutic use/adverse effects
*Arthritis, Rheumatoid/microbiology/immunology/therapy/diagnosis
Dysbiosis
Treatment Outcome
*Bacteria/immunology/growth & development/metabolism
Animals
*Intestines/microbiology/immunology
Host-Pathogen Interactions

@article {pmid40329496,
year = {2025},
author = {Rose, S and Johnson, H and Cartozzo, C and Swall, J and Simmons, T and Singh, B},
title = {Testing the efficacy of surface swab sampling to determine postmortem submersion interval (PMSI), using the microbiome colonization of skeletal remains.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.70039},
pmid = {40329496},
issn = {1556-4029},
abstract = {Postmortem interval (PMI) estimation contributes valuable information in the medicolegal investigation of decomposed human remains, and estimating the postmortem submersion interval (PMSI) can specifically aid investigations involving victims discovered in aquatic environments. Microbial succession-driven models in long-term decomposition studies have utilized the abundant colonizing bacterial community of skeletal remains to estimate the PMSI using bone powder. This study investigates the use of bone surface swabbing as an effective alternative method that minimizes time and resources required for bone sampling and also provides a highly replicable method for decomposition studies. Skeletal porcine (Sus scrofa) remains were caged and submerged in both lentic and lotic environments (Henley Lake in White Hall and James River at the Rice Rivers Center in Charles City, respectively) in Central Virginia from November 2017 to November 2018. Bone surface swabs and water samples were analyzed at 500 accumulated degree days (ADD) intervals, from baseline (0 ADD) to 4500 ADD. Variable region 4 (V4) of 16S rDNA was amplified and sequenced using the Illumina MiSeq Sequencing platform and analyzed using Mothur (v.1.39.5) and R (v.4.04). Analysis of Molecular Variance (AMOVA) indicated a significant difference in bacterial community structure among and between the swab, bone, and water samples (p < 0.001, F = 7.92331), and among and between lake and river samples (p < 0.001, F = 9.38829). PMSI models were constructed using random forest models for lake swabs (R[2] = 0.83, RMSE = 623.24) and river swabs (R[2] = 0.83, RMSE = 580.2). Swab samples from both aquatic environments predicted PMSI, albeit slightly less accurately than those previously reported from bone powder (lake: R[2] = 0.96, 334.1; river: R[2] = 0.94, 498.47).},
}

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

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

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

Humans
*Microbiota/genetics
Female
*Bacteria/genetics/classification/isolation & purification/drug effects
Male
Adult
Metagenomics/methods
*Oropharynx/microbiology
Middle Aged
*Drug Resistance, Microbial/genetics
Family Characteristics
Young Adult
Metagenome

@article {pmid40329425,
year = {2025},
author = {Vigneron, A and Cloarec, LA and Brochier-Armanet, C and Flandrois, JP and Troussellier, M and Bernard, C and Agogué, H and Oger, PM and Hugoni, M},
title = {Genomic characterisation of novel extremophile lineages from the thalassohaline lake Dziani Dzaha expands the metabolic repertoire of the PVC superphylum.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {48},
pmid = {40329425},
issn = {2524-6372},
support = {project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; project MARWEL, ANR-21-CE20-0049//Agence Nationale de la Recherche/ ; project SUBSILAKE, ANR-21-CE02-0027//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Extreme environments are useful systems to investigate limits of life, microbial biogeography and ecology, and the adaptation and evolution of microbial lineages. Many novel microbial lineages have been discovered in extreme environments, especially from the Planctomycetota-Verrucomicrobiota-Chlamydiota (PVC) superphyla. However, their evolutionary history and roles in ecosystem functioning and microbiome assemblage are poorly understood.

RESULTS: Applying a genome-centric approach on an 8-year metagenomic timeseries produced from the hypersaline and hyperalkaline waters of Lake Dziani Dzaha (Mayotte), we recovered 5 novel PVC extremophilic candidate lineages from the biosphere of the lake. Sibling to Elusimicrobia and Omnitrophota, these lineages represented novel halophilic clades, with global distributions bounded to soda lakes and hypersaline hydrosystems. Genome mining of these newly defined clades revealed contrasted, but ecologically relevant, catabolic capabilities involved in the carbon, hydrogen and iron/electron cycles of the Dziani Dzaha ecosystem. This also includes extracellular electron transfer for two of them, suggesting metal reduction or potential electron exchanges with other members of the lake community. By contrast, a putative extracellular giant protein with multiple carbohydrate binding domains and toxin-like structures, as observed in virulence factors, was identified in the genome of another of these clades, suggesting predatory capabilities.

CONCLUSIONS: Our results provided genomic evidences for original metabolism in novel extremophile lineages of the PVC superphyla, revealing unforeseen implications for members of this widespread and diverse bacterial radiation in aquatic saline ecosystems. Finally, monitoring the in-situ distribution of these lineages through the timeseries reveals the drastic effects of environmental perturbations on extreme ecosystem biodiversity.},
}

@article {pmid40329403,
year = {2025},
author = {Huang, Y and Cheng, S and Shi, J and He, P and Ma, Y and Yang, R and Zhang, X and Cao, Y and Lei, Z},
title = {Enhancing Holstein steers growth performance: oregano essential oil's impact on rumen development, functionality and microorganism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {44},
pmid = {40329403},
issn = {2524-4671},
support = {GSA-XMLZ-2021-01//Beef Cattle Quality Fattening Project of Gansu Province/ ; GSSLCSX-2020-1//Major Science and Technology Special Project of Gansu Province/ ; 2024CYZC-36//Industry Support Project of Gansu Province/ ; },
abstract = {BACKGROUND: Dietary supplementation with oregano essential oil (OEO), a natural plant extracts, is an effective and acceptable method to improve growth, beef quantity and quality, but the undergoing mechanism in rumen has not yet been reported in Holstein steers. This study investigated the effects of oregano essential oil (OEO) on growth performance, fermentation parameters, digestive enzymes activity, rumen development and microbiota in Holstein steers. Eighteen steers were randomly divided into two groups (n = 9) and fed either a basal diet (CCK) or the same diet supplemented with 20 g/(d·head) OEO (CEO) for 270 days.

RESULTS: OEO increased the rumen contents of volatile fatty acids (VFA, acetate (P = 0.011), propionate (P = 0.008), butyrate (P = 0.018)) and digestive enzymes activity (cellulase (P = 0.018), protease and β-glucosidase (P < 0.001)), and improved rumen development (papillae width (P = 0.008) and micropapillary density (P = 0.001)), which reasons contribute to increase body weight (BW, P = 0.022), average daily gain (ADG, P = 0.021), carcass weight (P = 0.001), dressing percentage (P < 0.001), and net meat production (P = 0.001) of steers. Meanwhile, metagenomic and metabolomic analysis revealed OEO significantly reduced abundance of rumen microorganisms, especially methanogenic archaea and viruses while beneficial bacteria (Bifidobacterium) and virulence factors were not affected. KEGG analysis revealed that OEO significantly reduces the host risk of disease, improves the digestive system, and reduces the energy basic metabolism level. A correlation analysis indicated fourteen kinds key microbiome and six downregulated metabolites interfere with each other and together influence the growth performance of steers.

CONCLUSION: These results suggest that feed with 20 g/(d·head) OEO in steers diets could improve growth performance, and reduces virus abundance and disease risk. And the findings provide fundamental insights into OEO, as an alternative source of natural bioactive compounds, how effect on rumen development, composition and function of microorganisms.},
}

@article {pmid40329366,
year = {2025},
author = {Wang, W and Gu, W and Schweitzer, R and Koren, O and Khatib, S and Tseng, G and Konnikova, L},
title = {In utero human intestine contains maternally derived bacterial metabolites.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {116},
pmid = {40329366},
issn = {2049-2618},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Placenta/microbiology/metabolism ; *Fetus/microbiology/metabolism ; *Intestines/microbiology ; Meconium/microbiology ; Decidua/microbiology/metabolism ; Intestinal Mucosa/metabolism/microbiology ; Host Microbial Interactions ; Metabolome ; },
abstract = {BACKGROUND: Understanding when host-microbiome interactions are first established is crucial for comprehending normal development and identifying disease prevention strategies. Furthermore, bacterially derived metabolites play critical roles in shaping the intestinal immune system. Recent studies have demonstrated that memory T cells infiltrate human intestinal tissue early in the second trimester, suggesting that microbial components such as peptides that can prime adaptive immunity and metabolites that can influence the development and function of the immune system are also present in utero. Our previous study reported a unique fetal intestinal metabolomic profile with an abundance of several bacterially derived metabolites and aryl hydrocarbon receptor (AHR) ligands implicated in mucosal immune regulation.

RESULTS: In the current study, we demonstrate that a number of microbiome-associated metabolites present in the fetal intestines are also present in the placental tissue, and their abundance is different across the fetal intestine, fetal meconium, fetal placental villi, and the maternal decidua. The fetal gastrointestinal samples and maternal decidua samples show substantially higher positive correlation on the abundance of these microbial metabolites than the correlation between the fetal gastrointestinal samples and meconium samples. The expression of genes associated with the transport and signaling of some microbial metabolites is also detectable in utero.

CONCLUSIONS: We suggest that the microbiome-associated metabolites are maternally derived and vertically transmitted to the fetus. Notably, these bacterially derived metabolites, particularly short-chain fatty acids and secondary bile acids, are likely biologically active and functional in regulating the fetal immune system and preparing the gastrointestinal tract for postnatal microbial encounters, as the transcripts for their various receptors and carrier proteins are present in second trimester intestinal tissue through single-cell transcriptomic data. Video Abstract.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
*Bacteria/metabolism/classification/genetics/isolation & purification
Placenta/microbiology/metabolism
*Fetus/microbiology/metabolism
*Intestines/microbiology
Meconium/microbiology
Decidua/microbiology/metabolism
Intestinal Mucosa/metabolism/microbiology
Host Microbial Interactions
Metabolome

@article {pmid40329211,
year = {2025},
author = {Sun, M and De Cuyper, A and Xu, J and Quiévy, A and Janssens, GPJ},
title = {Exploring fecal microbial activity in zoo felids of varying body mass on a similar diet.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {270},
pmid = {40329211},
issn = {1471-2180},
mesh = {Animals ; *Feces/microbiology/chemistry ; *Animals, Zoo/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Felidae/microbiology ; *Diet ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fatty Acids, Volatile/analysis ; Belgium ; DNA, Bacterial/genetics ; Phylogeny ; Sequence Analysis, DNA ; Male ; Body Weight ; },
abstract = {Under human care, felids are typically fed similar diets, unlike wild counterparts whose diets vary by body mass and ecology. This study evaluated fecal microbiota and fermentation products in 18 zoo felids from Pairi Daiza Zoo, Belgium, grouped by body mass: under 100 kg ("small") and over 100 kg ("large"), with 9 animals in each group. Fresh feces were collected from the rectum under anesthesia. Microbial composition was assessed via 16S rRNA gene sequencing, while the fecal volatile fatty acids were quantified using gas chromatography. At the phylum level, regardless of body mass, the gut microbiota of zoo felids was predominantly composed of Firmicutes (61.7%), Actinobacteria (16.4%) and Bacteroidetes (12.5%). At the genus level, the most abundant genus was Clostridium sensu stricto 1 (15.9%), followed by Collinsella (15.7%). Although no significant differences in microbial composition or alpha diversity were found, beta diversity showed body mass influenced overall microbial structure. Smaller felids had significantly higher acetate levels than larger felids (p < 0.01). Additionally, acetate proportions were positively correlated with Clostridium sensu stricto 13 (r = 0.6, p < 0.01) and Peptoniphilus (r = 0.5, p < 0.05). These results show particular associations between body mass and the response of the intestinal microbiome to diet, suggesting that a uniform diet may not suit all felids under human care.},
}

Animals
*Feces/microbiology/chemistry
*Animals, Zoo/microbiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Felidae/microbiology
*Diet
*Bacteria/classification/genetics/isolation & purification/metabolism
Fatty Acids, Volatile/analysis
Belgium
DNA, Bacterial/genetics
Phylogeny
Sequence Analysis, DNA
Male
Body Weight

@article {pmid40329182,
year = {2025},
author = {Cheng, S and Chu, X and Wang, Z and Khan, A and Tao, Y and Shen, H and Yang, P},
title = {Uncovering potential biomarkers and metabolic pathways in systemic lupus erythematosus and lupus nephritis through integrated microbiome and metabolome analysis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {275},
pmid = {40329182},
issn = {1471-2180},
support = {82202600//the National Natural Science Foundation of China/ ; 2024-LCYJ-MS-11//the Nanjing Drum Tower Hospital Clinical Research Special Fund Project/ ; XJSFZJJ201905//the New Technology Development Fund of Nanjing Drum Tower Hospital/ ; },
mesh = {Humans ; *Lupus Nephritis/microbiology/metabolism ; *Lupus Erythematosus, Systemic/microbiology/metabolism ; Biomarkers/metabolism/analysis ; Adult ; Female ; *Gastrointestinal Microbiome ; *Metabolome ; Male ; RNA, Ribosomal, 16S/genetics ; *Metabolic Networks and Pathways ; Feces/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Metabolomics/methods ; Young Adult ; Case-Control Studies ; },
abstract = {OBJECTIVE: This study aims to explore the relationship between gut microbiota and fecal metabolomic profiles in patients with systemic lupus erythematosus (SLE), with and without lupus nephritis (LN), in order to identify potentially relevant biomarkers and better understand their association with disease progression.

METHODS: Fecal samples from 15 healthy controls (HC) and 36 SLE patients (18 SLE-nonLN and 18 SLE-LN) were analyzed using 16S rRNA gene sequencing and untargeted metabolomics. Differential microbial taxa and metabolites were identified using Linear Discriminant Analysis Effect Size (LEfSe) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Receiver Operating Characteristic (ROC) curve analyses were used to assess the potential clinical relevance of selected metabolites.

RESULTS: Beta diversity analysis demonstrated distinct microbial clustering between groups (p < 0.05). SLE-LN samples showed an increased relative abundance of Proteobacteria and decreased Firmicutes compared to SLE-nonLN. Metabolomic profiling identified multiple differentially abundant metabolites, with notable enrichment in primary bile acid biosynthesis pathways (e.g., Glycocholic acid, AUC = 0.951). In the SLE-nonLN group, increased Glycoursodeoxycholic acid levels (AUC = 0.922) were observed in pathways related to taurine and hypotaurine metabolism. Correlation analysis indicated a negative association between Escherichia-Shigella and bile acid levels (p < 0.01).

CONCLUSION: This integrative analysis suggests that patients with SLE and LN harbor distinct gut microbiota and metabolomic profiles. The identified microbial taxa and metabolites may have potential as non-invasive biomarkers and could contribute to a better understanding of SLE pathogenesis and progression.},
}

Humans
*Lupus Nephritis/microbiology/metabolism
*Lupus Erythematosus, Systemic/microbiology/metabolism
Biomarkers/metabolism/analysis
Adult
Female
*Gastrointestinal Microbiome
*Metabolome
Male
RNA, Ribosomal, 16S/genetics
*Metabolic Networks and Pathways
Feces/microbiology/chemistry
*Bacteria/classification/genetics/metabolism/isolation & purification
Middle Aged
Metabolomics/methods
Young Adult
Case-Control Studies

@article {pmid40329009,
year = {2025},
author = {Nobels, A and van Marcke, C and Jordan, BF and Van Hul, M and Cani, PD},
title = {The gut microbiome and cancer: from tumorigenesis to therapy.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40329009},
issn = {2522-5812},
support = {T.0032.25//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; EOS: program no. 40007505//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; WELBIO-CR-2022A-02//Fonds De La Recherche Scientifique - FNRS (Belgian National Fund for Scientific Research)/ ; },
abstract = {The gut microbiome has a crucial role in cancer development and therapy through its interactions with the immune system and tumour microenvironment. Although evidence links gut microbiota composition to cancer progression, its precise role in modulating treatment responses remains unclear. In this Review, we summarize current knowledge on the gut microbiome's involvement in cancer, covering its role in tumour initiation and progression, interactions with chemotherapy, radiotherapy and targeted therapies, and its influence on cancer immunotherapy. We discuss the impact of microbial metabolites on immune responses, the relationship between specific bacterial species and treatment outcomes, and potential microbiota-based therapeutic strategies, including dietary interventions, probiotics and faecal microbiota transplantation. Understanding these complex microbiota-immune interactions is critical for optimizing cancer therapies. Future research should focus on defining microbial signatures associated with treatment success and developing targeted microbiome modulation strategies to enhance patient outcomes.},
}

@article {pmid40267994,
year = {2025},
author = {Tschann, MM and Vachharajani, V and Redmond, EM and Hoisington, A and Cohen, SE and New-Aaron, M and Llorente, C and Paloczi, J and Keating, CR and Rungratanawanich, W and Burnham, EL and Callaci, JJ and Raju, P and Zhong, W and Mandal, A and Zimmerly, JR and Nuncio, ASP and Mandrekar, P and McCullough, RL and McMahan, RH and Wyatt, TA and Yeligar, SM and Kovacs, EJ and Choudhry, MA},
title = {New developments on the effects of alcohol use on immunity, inflammation and organ function: A summary of the 2024 Alcohol and Immunology Research Interest Group (AIRIG) meeting.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {126},
number = {},
pages = {1-10},
doi = {10.1016/j.alcohol.2025.04.002},
pmid = {40267994},
issn = {1873-6823},
abstract = {The 29th annual Alcohol and Immunology Research Interest Group (AIRIG) meeting was held on November 22nd, 2024, at Loyola University Chicago, Health Science Campus, Maywood, Illinois. The meeting was divided into three plenary sessions and a poster session. The overall focus of this year's meeting was on alcohol and host immunity, alcohol and organ dysfunction, and alcohol, inflammation, and tissue injury. The presentations in each session shared the latest developments on the impact of alcohol in a wide variety of fields including trauma, emergency care and hospitalization, cardiovascular health, neurodegenerative disease, gut microbiome, and hepatology.},
}

@article {pmid40329006,
year = {2025},
author = {Britos, M and Hernández, M and Fernández, A and Pellegrini, E and Chaparro, L and Chaparro, A and Suárez, LJ and Hoare, A and Hernández-Ríos, P},
title = {Bacterial translocation signatures and subgingival microbiome in individuals with periodontitis.},
journal = {Clinical oral investigations},
volume = {29},
number = {6},
pages = {288},
pmid = {40329006},
issn = {1436-3771},
abstract = {OBJECTIVES: To determine bacterial blood translocation signatures and their association with the subgingival microbiota in individuals with and without periodontitis.

MATERIALS AND METHODS: Cross-sectional study. DNA was extracted from blood and subgingival samples of individuals with periodontitis (n = 21) and control volunteers (n = 24). Subgingival microbiota was explored by 16 S rRNA gene sequencing. Detection frequency and loads of total bacteria, Porphyromonas gingivalis (Pg), Porphyromonas endodontalis (Pe) and Fusobacterium nucleatum (Fn) were determined in all samples using quantitative polymerase chain reaction (qPCR). The statistical analysis was performed using STATA 16.

RESULTS: Subgingival samples from individuals with periodontitis presented higher relative abundance of Prevotella intermedia, F. nucleatum subsp. vincentii, Treponema sp. HMT 237, Alloprevotella tannerae, Filifactor alocis, Pg, Treponema denticola and Pe, and higher loads of total bacteria, Pg, Pe and Fn, compared to the control group (p < 0.001). While Pg and Fn were not detected in blood, Pe was detected in 95% of individuals with periodontitis and 83% of the control ones (p = 0.205), with higher loads in blood samples from periodontitis (p = 0.034). No significant correlation was found between subgingival bacterial loads and blood loads of Pe in periodontitis and control groups (p > 0.05).

CONCLUSIONS: Individuals with periodontitis presented higher relative abundance and loads of periodontal bacteria in subgingival samples and higher Pe loads in blood samples, although further research is needed to understand the correlation between subgingival and blood bacterial loads.

CLINICAL RELEVANCE: The present study showed higher loads of Pe in the blood of individuals with periodontitis, suggesting potential extraoral dissemination and a linking mechanism with several systemic diseases.},
}

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

@article {pmid40328942,
year = {2025},
author = {},
title = {Microbiome ageing in genetically diverse mice.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1032-1033},
pmid = {40328942},
issn = {2058-5276},
}

@article {pmid40328941,
year = {2025},
author = {},
title = {Call for papers on the clinical microbiome.},
journal = {Nature microbiology},
volume = {10},
number = {5},
pages = {1027},
pmid = {40328941},
issn = {2058-5276},
}

@article {pmid40328908,
year = {2025},
author = {Bowie, KR and Garzotto, M and Orwoll, E and Karstens, L},
title = {Body mass index and benign prostatic hyperplasia correlate with urinary microbiome diversity and lower urinary tract symptoms in men.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {159},
pmid = {40328908},
issn = {2730-664X},
support = {K01DK116706//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01DK138121//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01AG066671//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; UL1 TR000128/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65-90 years from the Osteoporotic Fractures in Men (MrOS) study.

METHODS: Bacterial DNA was isolated from urine samples. The V4 region of the 16S rRNA gene was sequenced using Illumina Miseq. Microbiome characteristics, including diversity measures and urotypes, are examined for associations with clinical characteristics and lower urinary tract symptoms.

RESULTS: Here we identify significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis reveals complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome.

CONCLUSIONS: By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.},
}

@article {pmid40328737,
year = {2025},
author = {Hitch, TCA and Masson, JM and Pauvert, C and Bosch, J and Nüchtern, S and Treichel, NS and Baloh, M and Razavi, S and Afrizal, A and Kousetzi, N and Aguirre, AM and Wylensek, D and Coates, AC and Jennings, SAV and Panyot, A and Viehof, A and Schmitz, MA and Stuhrmann, M and Deis, EC and Bisdorf, K and Chiotelli, MD and Lissin, A and Schober, I and Witte, J and Cramer, T and Riedel, T and Wende, M and Winter, KA and Amend, L and Riva, A and Trinh, S and Mitchell, L and Hartman, J and Berry, D and Seitz, J and Bossert, LC and Grognot, M and Allers, T and Strowig, T and Pester, M and Abt, B and Reimer, LC and Overmann, J and Clavel, T},
title = {HiBC: a publicly available collection of bacterial strains isolated from the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4203},
pmid = {40328737},
issn = {2041-1723},
support = {513892404//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains are accessible to the scientific community. We have therefore created a publicly available collection of bacterial strains isolated from the human gut. The Human intestinal Bacteria Collection (HiBC) (https://www.hibc.rwth-aachen.de) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.},
}

@article {pmid40328731,
year = {2025},
author = {Wei, C and Xu, X and Zhang, J and Wang, X and Han, T and Zhang, Y and Pan, S and Ming, Z and Li, R and Lou, F and Cheng, Y and Xu, H and Sun, X and Geng, G and Pan, Y and Liu, Q and Qi, H and Yan, X and Dang, K and Zhou, J and Sun, C and Li, Y},
title = {Timing of unsaturated fat intake improves insulin sensitivity via the gut microbiota-bile acid axis: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4211},
pmid = {40328731},
issn = {2041-1723},
support = {Key Program 82030100//National Natural Science Foundation of China (National Science Foundation of China)/ ; Joint Fund Project U24A20768//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The timing of dietary total fat intake influences glucose homeostasis, however, the impact of unsaturated fat (USFA) intake has yet to be explored. This 12-week, double-blind, randomized, controlled, 2 × 2 factorial-designed feeding trial investigated the effects of timing (lunch or dinner) and types of dietary USFA (high monounsaturated fat or polyunsaturated fat diet) intake on glucose metabolism in seventy prediabetes participants (mean age, 57 years). Sixty participants with completed fecal samples were included in the final analysis (n = 15 for each group). Postprandial serum glucose was first primary outcome, postprandial insulin levels and insulin sensitivity indices were co-primary outcomes Secondary outcomes were continuous glucose levels, serum fatty acid profile, gut microbiome (metagenomic sequencing) and fecal metabolites. Results showed no significant differences in postprandial glucose between groups. However, USFA intake at lunch (vs. dinner) improved insulin sensitivity and reduced postprandial insulin and serum free saturated fatty acid (Ptiming < 0.05, Ptype > 0.05, Pinteraction > 0.05), which was associated with alterations in gut microbiome and bile acid metabolism, regardless of USFA type. In summary, these results suggest that advancing timing of USFA intake improves insulin sensitivity through the gut microbiome and bile acid metabolism. Trial registration: ChiCTR2100045645.},
}

@article {pmid40328175,
year = {2025},
author = {Hansen, B and Sánchez-Castro, M and Schintgen, L and Khakdan, A and Schneider, JG and Wilmes, P},
title = {The impact of fasting and caloric restriction on rheumatoid arthritis in humans: A narrative review.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {49},
number = {},
pages = {178-186},
doi = {10.1016/j.clnu.2025.04.025},
pmid = {40328175},
issn = {1532-1983},
abstract = {Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease affecting approximately 1 % of the global population. It is characterized by swollen and painful joints eventually evolving into bone erosion, cartilage degradation and systemic inflammation, that significantly reduce patients' quality of life. While modern pharmacological treatments often lead to symptom improvement, they are also accompanied by substantial side effects, which can further impair patient wellbeing. Dietary interventions, particularly fasting and caloric restriction (CR), have gained increasing attention as adjunctive strategies for RA prevention and treatment. Their anti-inflammatory potential and ability to modulate the gut microbiome render them an attractive option to accompany or modify medical treatment. However, high-quality research on fasting and CR interventions in humans with RA remains limited, and the underlying mechanisms are not yet fully understood. The present narrative review reflects our current knowledge regarding fasting and CR, emphasising their impact on clinical outcomes, potential underlying mechanism and the sustainability of their effects. Evidence suggests that fasting and CR may lead to short-term improvements in RA disease activity, including reductions in inflammatory markers such as C-reactive protein (CRP) and interleukin-6 (IL-6). However, their long-term efficacy remains uncertain due to the limited duration of most studies. Future research should focus on identifying optimal fasting and CR protocols and their feasibility in long-term disease management, along with investigating patient adherence and potential risks associated with fasting interventions.},
}

@article {pmid40328070,
year = {2025},
author = {Jebali, A and Kaur, H and Martinez, H and Getto, S and Gleasner, C and Echenique-Subiabre, I and Gerber, J and Holguin, FFO and Nalley, J and O'Kelly, CJ and Shurin, JB and Starkenburg, SR and Corcoran, AA},
title = {Two years of outdoor cultivation in alternate climates produces little divergence in the productivity of Nannochloropsis.},
journal = {The Science of the total environment},
volume = {981},
number = {},
pages = {179587},
doi = {10.1016/j.scitotenv.2025.179587},
pmid = {40328070},
issn = {1879-1026},
abstract = {Local environmental conditions may act as driving forces of natural selection and lead to trait divergence through time in outdoor microalgae cultures. In addition, microalgae phenotypes expressed outdoors may be modulated by other organisms, including pests and associated microbial communities. The present work builds on the long-term cultivation of a Nanochloropsis strain, across four geographically distinct field sites. The strain showed enhanced productivity at a site in California and decreased productivity at a site in New Mexico. The goal of the present work was to determine if those trait differences, among others, were the result of natural selection and evolution, phenotypic plasticity, or changes due to the influence of local microbiomes. To accomplish this goal, we coupled an outdoor common garden experiment in which cultivars from all four sites were grown at a single site in New Mexico with analyses of the algal microbiome. Our work revealed no differences in biomass productivity or biomass composition across strains in a common garden, suggesting that the parent strain exhibits high phenotypic plasticity, allowing growth across a wide range of climatic conditions. With respect to the microbiome, community composition and richness differed across cultivation system scales, parent and replicate ponds, and with and without pest management - but not greatly within the common garden. Our findings suggest that Nannochloropsis plasticity was driving the variation in phenotypic productivity responses to site-specific conditions and disturbances. This study helps in understanding the phenotypic changes and microbial community dynamics over years of cultivation.},
}

@article {pmid40327993,
year = {2025},
author = {Grafakou, ME and Pferschy-Wenzig, EM and Aziz-Kalbhenn, H and Kelber, O and Moissl-Eichinger, C and Bauer, R},
title = {Bidirectional interactions between St. John´s wort and gut microbiome: Potential implications on gut-brain-axis.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {187},
number = {},
pages = {118111},
doi = {10.1016/j.biopha.2025.118111},
pmid = {40327993},
issn = {1950-6007},
abstract = {Emerging evidence highlights the role of gut microbiome in mental health disorders, including depression, raising the question whether the action of antidepressants could be mediated, at least in part, via the microbiome-gut-brain axis. To explore this, we subjected a St. John's wort extract (STW 3-VI), clinically proven to be effective in mild to moderate depression, to a model of the upper and lower intestinal tract, including static in vitro predigestion followed by ex vivo incubation with human microbiota samples. To cover the interindividual diversity of gut microbiome composition, fecal samples from ten healthy volunteers were used. Although unchanged levels of most annotated compounds were observed during simulated upper intestinal tract digestion, incubation with fecal microbiota led to a significant change of the chemical profile of the extract. While hyperforins remained stable, flavonoids and hypericins were rapidly biotransformed, suggesting that they may act as prodrugs. Several metabolites were formed, many of which are known to be involved in gut-brain communication. Differential abundance analysis revealed significant changes in microbiome composition, particularly for taxa known to be potentially associated with depression. Among others, the Firmicutes/Bacteroidetes ratio, known to be lowered in depressive patients, was increased. Functional profiling revealed modulation of pathways involved in gut-brain communication, such as tyrosine and tryptophan metabolism. These bidirectional interactions suggest for the first time the gut microbiome as a potential mediator of the pharmacological effects of St. John's wort extracts via the microbiome-gut-brain axis.},
}

@article {pmid40327698,
year = {2025},
author = {Clegg, T and Gross, T},
title = {Cross-feeding creates tipping points in microbiome diversity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {19},
pages = {e2425603122},
doi = {10.1073/pnas.2425603122},
pmid = {40327698},
issn = {1091-6490},
mesh = {*Microbiota/physiology ; *Biodiversity ; *Models, Biological ; },
abstract = {A key unresolved question in microbial ecology is how the extraordinary diversity of microbiomes emerges from the interactions among their many functionally distinct populations. This process is driven in part by the cross-feeding networks that help to structure these systems, in which consumers use resources to fuel their metabolism, creating by-products which can be used by others in the community. Understanding the effects of cross-feeding presents a major challenge, as it creates complex interdependencies between populations which can be hard to untangle. We address this problem using the tools of network science to develop a structural microbial community model. Using methods from percolation theory, we identify feasible community states for cross-feeding network structures in which the needs of consumers are met by metabolite production across the community. We identify tipping points at which small changes in structure can cause the catastrophic collapse of cross-feeding networks and abrupt declines in microbial community diversity. Our results are an example of a well-defined tipping point in a complex ecological system and provide insight into the fundamental processes shaping microbiomes and their robustness. We further demonstrate this by considering how network attacks affect community diversity and apply our results to show how the apparent difficulty in culturing the microbial diversity emerges as an inherent property of their cross-feeding networks.},
}

*Microbiota/physiology
*Biodiversity
*Models, Biological

@article {pmid40327666,
year = {2025},
author = {Yang, X and Zhang, Y and Xu, Y and Xu, Y and Zhang, M and Guan, Q and Hu, W and Tun, HM and Xia, Y},
title = {Microbial Disturbances Caused by Pesticide Exposure and Their Predictive Implications for Gestational Diabetes Mellitus.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01076},
pmid = {40327666},
issn = {1520-5851},
abstract = {Previous studies have suggested that pesticide exposure and gut microbiome alterations are associated with gestational diabetes mellitus (GDM) risk. Understanding the complex interactive effect of these factors on GDM is essential. In a cohort of 852 pregnant women, we assessed pesticide levels in serum and analyzed the gut microbiota using 16S rRNA and shotgun metagenomic sequencing. We explored the interactions between pesticides and gut microbiota, assessed their roles in GDM development, and proposed a predictive model based on identified biomarkers. We identified an environmental risk score (ERS), denoting the pesticide mixture level significantly associated with GDM, with the gut microbiota, particularly involving the Dorea branch, playing a crucial mediating role. In addition, we found an interactive effect of pesticide exposure and gut microbiota on GDM risk. Notably, low Prevotella enrichment combined with high ERS arisen from pesticide levels led to a 10.36-fold increased GDM risk. The identified pesticide and gut microbial biomarkers achieved high predictive accuracy for GDM (AUC: 0.833, 95% CI: 0.748-0.918). Collectively, maternal pesticide exposure may induce disrupted microbiome-dependent glycemic alteration, necessitating future assessment of clinical implications. Potential GDM markers can serve as targets for therapeutic intervention caused by pesticides, leading to prevention.},
}

@article {pmid40327389,
year = {2025},
author = {Leroue, MK and Maddux, AB and Lehmann, T and Niemiec, S and Mancuso, CA and Khailova, L and Mourani, PM and Klawitter, J and Davidson, JA},
title = {Alteration in Indole Metabolites After Cardiopulmonary Bypass Surgery in Neonates and Infants.},
journal = {Critical care explorations},
volume = {7},
number = {5},
pages = {e1267},
doi = {10.1097/CCE.0000000000001267},
pmid = {40327389},
issn = {2639-8028},
mesh = {Humans ; *Cardiopulmonary Bypass/adverse effects ; Infant, Newborn ; Infant ; Prospective Studies ; Male ; Female ; *Indoles/metabolism/blood ; Length of Stay/statistics & numerical data ; *Gastrointestinal Microbiome/physiology ; Indoleacetic Acids/blood ; },
abstract = {IMPORTANCE: Cardiopulmonary bypass (CPB) surgery is associated with changes in the intestinal microbiome. Metabolism of tryptophan into the indole pathway is entirely facilitated by the intestinal microbiome, and indole metabolites play a critical role in intestinal epithelial integrity, intestinal and systemic vascular tone, and intestinal and systemic immune response.

OBJECTIVES: To evaluate the impact of CPB on microbial-derived indole metabolites and their association with clinical outcomes.

Prospective cohort study of neonates and infants younger than 6 months of age undergoing CPB at a quaternary children's hospital.

MAIN OUTCOMES AND MEASURES: Serum samples underwent quantitative pathway mapping via mass spectroscopy. Clinical outcomes of interest included cardiac ICU (CICU) length of stay and Vasoactive-Inotropic Score (VIS) at 48 hours.

RESULTS: Ninety patients between 2 and 169 days old were enrolled. Patients showed significant postoperative changes in seven of eight indole metabolites. A two-fold increase in preoperative levels of indole-3-carboxylic acid was associated with 0.63 odds of requiring vasoactive medications at 48 hours (p = 0.023) and among those subjects still requiring vasoactives at 48 hours, they had an average 7.1% decrease in VIS at 48 hours (p = 0.005), and a 12.25% reduction in CICU length of stay (p = 0.001). Higher levels of indole-3-carboxylic acid preoperatively and at 24 and 48 hours postoperatively were also significantly associated with decreased CICU length of stay. Conversely, increased levels of several metabolites, including indole-3-lactic acid, indole-3-carbaldhyde, indole-3-propionic acid, tryptamine, and tryptophol, in the preoperative and postoperative period were associated with higher VIS at 48 hours and increased CICU length of stay.

CONCLUSIONS AND RELEVANCE: CPB was associated with significant changes in indole metabolite levels postoperatively. Indole-3-carboxylic acid, which suppresses T-regulatory (Treg) differentiation, is associated with improved patient outcomes, whereas other metabolites, that promote Treg differentiation, were associated with worse outcomes.},
}

Humans
*Cardiopulmonary Bypass/adverse effects
Infant, Newborn
Infant
Prospective Studies
Male
Female
*Indoles/metabolism/blood
Length of Stay/statistics & numerical data
*Gastrointestinal Microbiome/physiology
Indoleacetic Acids/blood

@article {pmid40327311,
year = {2025},
author = {Li, MJ and Chen, HM and Chen, YL and Lai, YH and Lai, CY and Ruan, JW and Chen, JW and Tsai, WH and Ko, WC and Tsai, PJ},
title = {Lactiplantibacillus plantarum GMNL-661 Ameliorates Clostridioides difficile Infection and Reconfigures Intestinal Microbiota in a Murine Model.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40327311},
issn = {1867-1314},
support = {NSTC 111-2320-B-006 -046 -MY3//National Science and Technology Council/ ; NSTC 111-2320-B-006 -046 -MY3//National Science and Technology Council/ ; NSTC 111-2320-B-006 -046 -MY3//National Science and Technology Council/ ; NSTC 111-2320-B-006 -046 -MY3//National Science and Technology Council/ ; NSTC 112-2314-B-006 -043 -MY3//National Science and Technology Council/ ; NSTC 111-2320-B-006 -046 -MY3//National Science and Technology Council/ ; },
abstract = {Clostridioides difficile infection (CDI) is a significant global health threat, often resulting from antibiotic-induced disruption of the gut microbiota, which leads to severe gastrointestinal issues. Current treatments, such as vancomycin, are effective but can cause subsequent relapses, further microbiota disruption, and high treatment costs. Probiotics offer a promising microbiota-based therapeutic strategy. Following an in vitro screening for novel lactic acid bacterial (LAB) strains with strong anti-C. difficile ability and good tolerance to digestive challenges, Lactiplantibacillus plantarum GMNL-661 emerged as a potential solution to combat CDI. In a CDI mice model, the appropriate dose of GMNL-661 effectively alleviated CDI, which caused weight loss, gut inflammation, and mucin depletion. GMNL-661 alleviated CDI symptoms through increased gut barrier genes and downregulated IL-1 and IL-18. 16s rDNA analysis of mice stool from CDI and CDI supplemented with GMNL-661 showed distinct microbiota ecology. GMNL-661 dramatically affected the microbiome of CDI, increasing Lactobacillus spp. and Clostridium cluster XVIII while reducing Clostridium and Enterococcus species. Genome analysis of GMNL-661 revealed minimal safety concerns in antibiotic resistance and virulence genes, confirming that it is suitable for inclusion in the food chain. Antimicrobial peptide (AMP) prediction on GMNL-661 and 299v genome suggested a strong potential candidate for anti-CD antimicrobial peptides. These findings highlighted L. plantarum GMNL-661 as an effective and highly safe therapeutic agent against CDI in clinical.},
}

@article {pmid40327219,
year = {2025},
author = {Jiang, WH and Zhao, XW and Jin, XM and Wang, WJ and Chen, Z},
title = {Mixed Infections in the Female Lower Genital Tract: Unlocking the Current Landscape and Future Directions.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {40327219},
issn = {2523-899X},
support = {No. 81874483//National Natural Science Foundation of China/ ; },
abstract = {Understanding mixed infections in the female lower genital tract is a critical challenge in modern infection research. The interplay of multiple pathogens complicates disease progression, often resulting in treatment failure, recurrent infections, and significant public health and economic burdens. These infections are further exacerbated by disrupted host immune responses, which hinder the recovery of the vaginal microecosystem. Additionally, microbial biofilms-a fundamental mode of pathogen coexistence-contribute to the persistence and drug resistance of these infections, complicating management strategies. This review examines the pathogenesis, diagnosis, and treatment of mixed infections in the female lower genital tract while exploring potential avenues for future research. These findings emphasize the need for greater focus on these infections and offer insights to enhance further research in this area.},
}

@article {pmid40327160,
year = {2025},
author = {Li, N and Gao, G and Zhang, T and Zhao, C and Zhao, Y and Zhang, Y and Sun, Z},
title = {Co-variation of Host Gene Expression and Gut Microbiome in Intestine-Specific Spp1 Conditional Knockout Mice.},
journal = {Current microbiology},
volume = {82},
number = {6},
pages = {282},
pmid = {40327160},
issn = {1432-0991},
support = {32325040//National Natural Science Foundation of China/ ; 2022BINCMCF007//Nutrition and Care of Maternal & Child Research Fund Project" of Biostime Institute of Nutrition & Care/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Osteopontin/genetics/metabolism ; Mice, Knockout ; Lipid Metabolism/genetics ; *Intestines/microbiology ; Mice, Inbred C57BL ; Transcriptome ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Osteopontin, which is a highly phosphorylated and glycosylated acidic secreted protein encoded by the secreted phosphoprotein 1 (Spp1) gene, plays a crucial role in immune regulation, inflammatory responses, and cell adhesion. However, its impact on intestinal gene expression and gut microbiota remains underexplored. In this study, we developed an Spp1 conditional knockout mouse model to investigate alterations in the intestinal transcriptome and microbiome, with particular emphasis on changes in gene expression and predicted metabolic pathways. Our findings demonstrated that Spp1 gene conditional knockout significantly modified the expression of genes involved in immune regulation and lipid metabolism. Moreover, metagenomic analysis revealed marked shifts in gut microbial diversity and predicted the metabolic pathways associated with digestion, absorption, and lipid metabolism. These results suggest that Spp1 is instrumental in maintaining gut microbial equilibrium and in regulating host lipid metabolism and immune responses. This study offers new insights into the role of Spp1 in host-microbiota interactions and the potential foundations for developing related therapeutic strategies.},
}

Animals
*Gastrointestinal Microbiome/genetics
Mice
*Osteopontin/genetics/metabolism
Mice, Knockout
Lipid Metabolism/genetics
*Intestines/microbiology
Mice, Inbred C57BL
Transcriptome
Bacteria/classification/genetics/isolation & purification

@article {pmid40327075,
year = {2025},
author = {Bukhari, Y and Chow, R and Xiang, AJ and Lemos, N},
title = {Long-Term Antibiotics for Disturbed Bladder Microbiome Disorders.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {40327075},
issn = {1433-3023},
abstract = {INTRODUCTION AND HYPOTHESIS: In recent years, there has been significant progress in understanding bladder disorders and their connection to the bladder microbiome. Emerging evidence suggests that the bladder microbiome, which is unique to each individual, plays a pivotal role in maintaining bladder health. Disruptions to the normal microbiome composition have been associated with various pathological conditions such as recurrent urinary tract infections, interstitial cystitis, and chronic recalcitrant cystitis.

METHODS: We completed a focused literature review to collect studies that evaluated the use of antibiotics for long-term treatment (more than 28 days) of infectious/inflammatory disturbed bladder microbiome DBM disorders.  RESULTS: This article reviews current literature on the composition of the bladder microbiome, describes the disorders associated with DBM, explores the utility of long-term antibiotics in managing DBM, and foresees future venues for DBM disorders research.

CONCLUSION: This review has demonstrated encouraging outcomes regarding the use of long-term antibiotics in managing infectious disorders of DBM, such as recurrent urinary tract infections and chronic recalcitrant cystitis, while no benefit was seen in interstitial cystitis patients. The studies showed that long-term cephalexin, fluoroquinolones, and fosfomycin are well-tolerated and effective options, with cephalexin being favored given its low side-effect profile.},
}

@article {pmid40327022,
year = {2025},
author = {Zhao, S and Yang, H and Lv, A and Zhang, S and Hui, Y and Qi, W and Zhao, H and Miao, M and Wang, Y and Yin, Y and Wang, Q and Chen, S and Wang, X},
title = {Vaginal Microbiome and Metabolome Profiles Among HPV Positive and HPV Negative Women Based on Stratification of Vaginitis.},
journal = {Journal of medical virology},
volume = {97},
number = {5},
pages = {e70385},
doi = {10.1002/jmv.70385},
pmid = {40327022},
issn = {1096-9071},
support = {//This study was supported by National High Level Hospital Clinical Research Funding (BJ-2023-208) and the Capital Health Research and Development of Special Project (2022-2Z-4055)./ ; },
mesh = {Humans ; Female ; *Vagina/microbiology/virology ; Adult ; *Metabolome ; *Microbiota ; *Papillomavirus Infections/microbiology/virology/metabolism ; Case-Control Studies ; *Vaginitis/microbiology/virology/metabolism ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Chromatography, Liquid ; Papillomaviridae/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {This study investigated the differences in vaginal microbiota and metabolism between HPV positive and HPV negative women based on the stratification of vaginitis. This was a case-control study. A total of 164 women were included in this study analysis with a ratio of 1:3 for HPV positive and HPV negative women. The V3-V4 region of the 16S rRNA gene was amplified by polymerase chain reaction (PCR) followed by sequencing with Illumina. Untargeted metabolomic sequencing was conducted by the liquid chromatography-mass spectrometry (LC-MS) system. Specific microbial species and differentially expressed metabolites associated with these differences were explored. We found that a statistically significant difference existed in the bacterial structure between HPV positive and HPV negative women (R = 0.2177, p = 0.001), and HPV positivity was associated with the enrichment of Lactobacillus iners among women diagnosed with vaginitis. However, this difference was not observed in women without vaginitis. Regarding metabolic differences, HPV positive women with vaginitis displayed elevated levels of organic acids and their derivatives, accompanied by decreased lipid levels in their vaginal secretions. Conversely, HPV positive women without vaginitis showed higher lipid levels and lower concentrations of organic acids and their derivatives. Among women with vaginitis, Lactobacillus iners was positively correlated with biogenic amine, organic acids and derivatives and negatively correlated with kessyl glycol. Among women without vaginitis, Lactobacillus iners was negatively correlated with pelargonic acid. The disparity in the abundance and metabolites of vaginal microbiota between HPV positive and HPV negative women could be affected by whether the woman has been diagnosed with vaginitis. Metabolic differences indicated that antioxidant therapy holds promising prospects for potential application in the management and treatment of HPV infections. Further in-depth research into the molecular mechanisms is crucial for clarifying the precise role that vaginal microbiota and metabolites play in HPV infection.},
}

Humans
Female
*Vagina/microbiology/virology
Adult
*Metabolome
*Microbiota
*Papillomavirus Infections/microbiology/virology/metabolism
Case-Control Studies
*Vaginitis/microbiology/virology/metabolism
RNA, Ribosomal, 16S/genetics
Middle Aged
Young Adult
Chromatography, Liquid
Papillomaviridae/isolation & purification/genetics
Bacteria/classification/genetics/isolation & purification

@article {pmid40326765,
year = {2025},
author = {Lindner, BG and Graham, KE and Phaneuf, JR and Hatt, JK and Konstantinidis, KT},
title = {SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c03603},
pmid = {40326765},
issn = {1520-5851},
abstract = {Methodologies utilizing metagenomics are attractive to fecal source tracking (FST) aims for assessing the presence and proportions of various fecal inputs simultaneously. Yet, compared to established culture- or PCR-based techniques, metagenomic approaches for these purposes are rarely benchmarked or contextualized for practice. We performed shotgun sequencing experiments (n = 35) of mesocosms constructed from the water of a well-studied recreational and drinking water reservoir spiked with various fecal (n = 6 animal sources, 3 wastewater sources, and 1 septage source) and synthetic microbiome spike-ins (n = 1) introduced at predetermined cell concentrations to simulate fecal pollution events of known composition. We built source-associated genome databases using publicly available reference genomes and metagenome assembled genomes (MAGs) recovered from short- and long-read sequencing of the fecal spike-ins, and then created an associated bioinformatic tool, called SourceApp, for inferring source attribution and apportionment by mapping the metagenomic data to these genome databases. SourceApp's performance varied substantially by source, with cows being underestimated due to under sampling of cow fecal microbiomes. Parameter tuning revealed sensitivity and specificity near 0.90 overall, which exceeded all alternative tools. SourceApp can assist researchers with analyzing and interpreting shotgun sequencing data and developing standard operating procedures on the frontiers of metagenomic FST.},
}

@article {pmid40326581,
year = {2025},
author = {Kirschner, P and Pawlitzki, M and Hartung, HP and Meuth, SG},
title = {Immunology of multiple sclerosis: an update.},
journal = {Current opinion in neurology},
volume = {38},
number = {3},
pages = {180-187},
doi = {10.1097/WCO.0000000000001361},
pmid = {40326581},
issn = {1473-6551},
mesh = {Humans ; *Multiple Sclerosis/immunology ; Gastrointestinal Microbiome/immunology ; Epstein-Barr Virus Infections/immunology/complications ; Animals ; B-Lymphocytes/immunology ; },
abstract = {PURPOSE OF REVIEW: The immunological processes that lead to multiple sclerosis (MS) and occur during the progressive phase of the disease are manifold and still not well understood. This review summarizes new insights on this topic that were gained through recent studies with diverse scientific approaches.

RECENT FINDINGS: While genetic risk clearly contributes to MS, external factors play a key role in its pathogenesis as well. Epstein-Barr virus infection correlates significantly with MS risk and seems to be a major causal factor. Even though our knowledge on the human gut microbiome and its connection to the central nervous system is far from being complete, several studies have proven that the gut-brain axis influences neuroinflammation and disease progression in MS. It has become much clearer that MS is not solely a T cell-mediated disease but is also strongly driven by B cells and pathogenic antibodies. Beyond the peripheral immune cells, glial cells and their interactions with neurons are important players contributing to disease activity and progression in MS.

SUMMARY: Taken together, recent publications on immunological processes in the context of MS implicate a multitude of noncanonical mechanisms that need to be further explored regarding their interplay and contribution to the degenerative course of the disease.},
}

Humans
*Multiple Sclerosis/immunology
Gastrointestinal Microbiome/immunology
Epstein-Barr Virus Infections/immunology/complications
Animals
B-Lymphocytes/immunology

@article {pmid40326319,
year = {2025},
author = {Montevecchio, AB and Jones, KL and Galvão, KN and Casaro, S and Maunsell, F and Liu, T and Jeong, KC and Chebel, RC},
title = {Heat Abatement During the Pre-Weaning Period: Effects on the Nasal Microbiota of Holstein Male Calves.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf121},
pmid = {40326319},
issn = {1525-3163},
abstract = {Housing strategies to alleviate the negative effects of heat stress on the performance of pre-weaned dairy calves have become a focus of research in recent years. Experiments evaluating such strategies have focused on thermoregulatory responses, behavior, and performance. To date, no experiments have evaluated their effects on the microbiota of the upper respiratory tract. Understanding this relationship is crucial for assessing its impact on respiratory health, disease susceptibility, and calf well-being. We conducted an experiment to characterize nasal microbiota from calves housed outdoors, under a naturally-ventilated barn, with and without the provision of fans. The experiment was conducted in a commercial dairy in southern GA. Male Holstein calves (n = 60) were assigned randomly at birth (d 0) to 1 of 3 treatments: hutch outdoors with 50% of its area covered with plywood (control = 20), hutch in an open-sided barn with no supplemental cooling (SH = 21), and hutch in an open-sided barn with ceiling fans (SHF = 19), and followed until 68 d of age. Following the removal of obvious debris of the nostrils, nasal swabs were collected from all calves on week 5 (35 ± 8.9 d) and 9 (63 ± 3.2 d) of life and qPCR and 16S rRNA sequencing were performed. Treatment did not affect total bacterial 16S gene copy numbers or alpha diversity (i.e., Shannon and Simpson indexes) at 5 or 9 weeks of age. We observed differences, however, in the nasal microbiome structure at weeks 5 and 9 among treatments, with variations in the mean relative abundance (MRA) of certain bacterial genera. On week 5, SHF treatment had reduced MRA of Mycoplasma compared with control and SH treatments and greater MRA of Acinetobacter than calves in the SH treatment. On week 9, control calves had reduced MRA of Escherichia compared with SHF calves and greater Moraxella MRA compared with those in the SH and SHF treatments. We observed differences in nasal microbiome structure of pre-weaned dairy calves as a result of housing strategy. While the results presented herein suggest a potential link between housing conditions and the risk of respiratory disease, further research is necessary to investigate this hypothesis. Improved understanding of the impact of housing environment on respiratory health as well as on heat stress could help producers make informed management decisions to improve calf health and wellbeing.},
}

@article {pmid40326149,
year = {2025},
author = {Aragon, J and Weber, AM and Tipton, M and Thomsen, J and Ibrahim, H and Weishaar, K and Rao, S and Suchodolski, JS and Stockman, J and Ryan, EP and Nealon, NJ},
title = {Impacts of Vincristine and Prednisolone Chemotherapy on the Canine Gut Microbiota in Dogs Undergoing Treatment for Lymphoma.},
journal = {Veterinary and comparative oncology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vco.13063},
pmid = {40326149},
issn = {1476-5829},
support = {//Colorado State University: Department of Clinical Sciences- Center for Companion Animal Studies- Young Investigator Grant Program/ ; T32AI162691//National Institute of Allergy and Infectious Diseases of the National Institutes of Health/ ; //Eldred Foundation/ ; //United States Department of Agriculture-National Institute of Food and Agriculture Higher Education Multicultural Scholars Program/ ; },
abstract = {Chemotherapy can have adverse gastrointestinal effects in dogs and people. The objective of this study was to assess the impact of vincristine and prednisolone/prednisone, as part of a CHOP chemotherapy [cyclophosphamide, hydroxydaunorubicin, oncovin (vincristine) and prednisolone/prednisone] protocol, on gastrointestinal dysbiosis in dogs with lymphoma. We hypothesised the first week of chemotherapy (administration of vincristine and prednisolone/prednisone, VCR/Pred) produces compositional and functional shifts in the canine faecal microbiota that are associated with increased dysbiosis. Faecal samples from canine lymphoma patients (n = 25) were compared for microbiota and metabolites before (pre-chemotherapy) and after the first week of VCR/Pred (post-chemotherapy). A dysbiosis index (DI) was calculated for each dog via quantitative PCR of seven bacterial taxa established for altered ratios in canine gastrointestinal dysbiosis: Faecalibacterium, Turicibacter, Escherichia coli, Streptococcus, Blautia, Fusobacterium and Peptacetobacter hiranonis (formerly Clostridium hiranonis). There was a significant increase in the DI post-chemotherapy compared to pre-chemotherapy (p = 0.021) concurrent with a significant decrease in faecal P. hiranonis concentrations post-chemotherapy (p = 0.0003). 16S rRNA amplicon sequencing analysis revealed a significant decrease in Enterococcaceae post-chemotherapy (p = 0.013). Targeted faecal lipid profiling identified markers of host and bacterial metabolic dysfunction that were altered following chemotherapy, including significant decreases in arachidonate (p = 0.0015), nervonate (p = 0.027), cholestanol (p = 0.011) and campesterol (p = 0.0035). These findings support that shifts in gut microbiota structure and function may contribute to gastroenteritis in dogs following the first week of VCR/Pred. Gut dysbiosis measures are important for improved treatment options that alleviate gastrointestinal complications associated with chemotherapy in animals and people.},
}

@article {pmid40326091,
year = {2025},
author = {Ipek, ED and Basaloglu, H},
title = {Neuroprotective effects of Saccharomyces boulardii and bacterial probiotics in a rotenone-Induced rat model of Parkinson's disease.},
journal = {Folia morphologica},
volume = {},
number = {},
pages = {},
doi = {10.5603/fm.104808},
pmid = {40326091},
issn = {1644-3284},
abstract = {BACKGROUND: Recent evidence suggests that Parkinson's disease (PD) may originate in the gut and impact the central nervous system via the gut-brain axis, highlighting the significance of the gut microbiome. This study explores the neuroprotective potential of probiotics and their impact on CD163 expression in muscularis macrophages in a rat model of rotenone-induced PD.

MATERIALS AND METHODS: Forty-eight rats were divided into six groups: control, vehicle control, and PD induced by rotenone consisting of positive control (rotenone only), a yeast probiotic group (25 mg/kg Saccharomyces boulardii), a bacterial probiotic group (10⁹/cfu/day probiotics mixture), and a combined yeast-bacterial probiotic group (25 mg/kg Saccharomyces boulardii, 10⁹/cfu/day probiotics mixture). We performed motor evaluations, tyrosine hydroxylase immunohistochemistry, stereological neuron counting in the hippocampus and cerebellum, and analyzed CD163 expression in muscularis macrophages via flow cytometry. The obtained data were statistically analyzed.

RESULTS: Rotenone-treated groups exhibited severe motor dysfunctions. Tyrosine hydroxylase immunoreactivity in the corpus striatum was lower in all rotenone-treated groups but it was higher in those with probiotic supplementation than in the positive control group. Rotenone caused degenerative changes in hippocampal pyramidal neurons, while probiotics demonstrated neuroprotective effects. CD163 expression in muscularis macrophages was significantly increased in the rotenone-treated groups compared to the control and vehicle control group.

CONCLUSIONS: Our findings suggest that probiotics mitigate rotenone-induced neurodegeneration by preserving dopaminergic neurons and modulating gut-immune interactions. Determining the phenotypic characterization of muscularis macrophages is essential and their relationship with the microbiome may play significant role in neurodegenerative diseases.},
}

@article {pmid40325900,
year = {2025},
author = {Mandl, A and Zahurak, ML and Metri, NA and Shore, ND and Mao, S and McKay, RR and Taplin, ME and Szmulewitz, RZ and Maughan, BL and Reichert, ZR and Kessler, ER and Heath, EI and Dreicer, R and Stein, CA and Milne, GL and Sfanos, KS and Ernst, SE and Mummert, LA and Cruz-Lebrón, A and Michel, SLJ and Kane, MA and Hursey, M and Worth, MA and Wagner, WD and Eshleman, JR and Debeljak, M and Xu, L and Cao, H and Dowling, D and Marshall, CH and Markowski, MC and Denmeade, SR and Eisenberger, MA and Antonarakis, ES and Carducci, MA and Paller, CJ},
title = {Muscadine Grape Skin Extract in Biochemically Recurrent Prostate Cancer: A Randomized, Placebo-Controlled, Biomarker-Enriched Trial in Patients With the SOD2 Ala/Ala Variant.},
journal = {The Prostate},
volume = {},
number = {},
pages = {},
doi = {10.1002/pros.24903},
pmid = {40325900},
issn = {1097-0045},
support = {//This work was supported by the Department of Defense CDMRP: W81XWH-22-2-0024, ASCO YIA, ECOG Paul Carbone Fellowship, and a grant from the Community Foundation of the National Capital Region, as well as the Analytical Pharmacology Shared Resource of the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins (NIH grants P30 CA006973 and UL1 TR 001079, and the Shared Instrument Grant (1S10RR026824-01). Prostate Cancer Foundation Challenge Award 16CHAL13 supports the contributions of KSS. E.S.A. is partially supported by NCI grant P30 CA077598 and DOD grant W81XWH-22-2-0025. The study drug and placebo were provided, at no cost, by Muscadine Naturals Inc./ ; },
abstract = {BACKGROUND: Many patients with biochemically recurrent prostate cancer (BCRPC) prefer to delay androgen deprivation therapy (ADT) due to its adverse effects, highlighting the need for better-tolerated, effective alternatives. A subgroup analysis of our prior Phase II trial showed that muscadine grape skin extract (MPX) increased PSA doubling time (PSADT) in patients with SOD2 Ala/Ala variant which provided the rationale for this trial.

METHODS: This randomized, double-blind, placebo-controlled trial, conducted at 14 sites, evaluated patients with BCRPC and SOD2 Ala/Ala genotype. Patients received 4000 mg MPX or placebo daily. The primary endpoint was on-study PSA slope with comparisons between treatment arms. Secondary endpoints were PSADT, PSA response (≥ 50% decrease), and PSA progression free survival (PFS). Correlative studies included markers of oxidative stress and gastrointestinal microbiota composition.

RESULTS: At interim analysis, fifty-nine patients were randomized (MPX, n = 29; placebo, n = 30). On-study PSA slopes at 12, 24, 36, and 48 weeks showed no significant differences between the MPX and placebo arms (p = 0.49). The study was stopped due to futility. No significant differences were observed in PSADT, PSA response, median PSA PFS, or oxidative stress biomarkers. MPX was well-tolerated, with no grade 3-4 AEs attributable to the study drug. Microbiome analysis showed no significant differences in alpha diversity but revealed increased relative abundance of Roseburia faecis and Akkermansia muciniphila in the MPX group.

CONCLUSIONS: Although MPX supplementation had no significant effect on PSA slope in men with BCRPC and SOD2 Ala/Ala variant, this study provides a rigorous evaluation of a natural product and highlights the importance of well-designed clinical trials in advancing evidence-based integrative oncology.

TRIAL REGISTRATION: ClinicalTrials. gov, NCT03535675.},
}

@article {pmid40325891,
year = {2025},
author = {Weston, S and Algotar, A and Karjoo, S and Gabel, M and Kruszewski, P and Duro, D and Sankararaman, S and Wendel, D and Namjoshi, SS and Abdelhadi, RA and Kawatu, D and Corkins, MR and Sentongo, T},
title = {State-of-the-art review of blenderized diets-Status and future directions.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70048},
pmid = {40325891},
issn = {1536-4801},
support = {//None/ ; },
abstract = {This state-of-the-art review was produced by a multidisciplinary team composed of pediatric gastroenterology and nutrition healthcare providers to provide a comprehensive overview of the use of blenderized tube feeds (BTFs). The team developed 12 vital questions to address gaps in the current understanding and practice of using BTFs, then performed a comprehensive search of literature published between 2000 and 2023 using PubMed, MEDLINE, Embase databases, and an individual search of references. There was a scarcity of well-designed randomized clinical trials, and most of the studies were prospective or retrospective observational reports from heterogeneous patient demographics, varieties of BTFs, and medical conditions. Use of BTFs was associated with improved outcomes, including higher satisfaction, reduced gastroesophageal reflux, retching, gagging, constipation, frequency of hospitalization for respiratory disease, and greater diversity of the gut microbiome. However, homemade and commercially manufactured BTFs varied in nutrient composition and physical properties, such as viscosity, which posed challenges related to ease of administration and comparison of clinical outcomes. Therefore, whereas the use of BTFs as an alternative to standard commercial formulas has become increasingly popular, further evidence is warranted to provide guidelines on best practices for usage, monitoring, and comparing clinical outcomes. Pediatric dietitians and clinician practitioners must regularly monitor children receiving BTFs to ensure nutritional adequacy, optimize safe and effective delivery, and promote optimal growth. The team proposed future directions regarding best practices for using BTFs, primarily related to clinical application and nutritional outcomes in children and adolescents.},
}

@article {pmid40325622,
year = {2025},
author = {Huang, S and Wang, X and Wang, M and Lin, J and Ren, J and Lu, C and Fu, J and Zhang, Y and Wang, X and Xiao, J and Guo, J and Zhou, H},
title = {S-9-PAHSA Protects Against High-Fat Diet-Induced Diabetes-Associated Cognitive Impairment via Gut Microbiota Regulation.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {5},
pages = {e70417},
doi = {10.1111/cns.70417},
pmid = {40325622},
issn = {1755-5949},
support = {81671392//National Science Foundation/ ; 81871098//National Science Foundation/ ; shslczdzk02802//Shanghai Municipal Key Clinical Specialty/ ; 2021YFE0111800//National Key R&D Program of China/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice ; *Cognitive Dysfunction/etiology/prevention & control ; Male ; Mice, Inbred C57BL ; *Diabetes Mellitus, Experimental/complications ; *Stearic Acids/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/complications ; Blood Glucose/drug effects/metabolism ; },
abstract = {AIM: Diabetes-associated cognitive impairment (DACI) is a common complication of Type 2 diabetes mellitus (T2DM), with its mechanisms and treatments for DACI remaining incompletely clarified. This study investigated the protective efficacy of the novel lipid S-enantiomer of 9-palmitic acid esters of hydroxy stearic acids (S-9-PAHSA, S9P) in a high-fat diet-induced DACI mouse model.

METHODS: Mice were randomly assigned to three groups: normal diet (ND), high-fat diet (HFD), and HFD + 30 mg/kg/day S9P (HFD + S9P). Fasting blood glucose (FBG), intraperitoneal glucose tolerance test (IPGTT), and insulin tolerance test (ITT) were conducted to assess blood glucose homeostasis. Morris Water Maze and Y maze tests evaluated cognitive function, and neuronal status was examined through pathological analysis, Golgi staining, and transmission electron microscopy (TEM). Colonic barrier integrity was assessed using periodic acid-Schiff and Alcian blue staining (AB-PAS) and immunohistochemistry (IHC) staining. Intestinal microbiota composition was analyzed by 16S rDNA sequencing, and serum metabolic characteristics were determined by metabolomics sequencing.

RESULTS: S9P improved glucose homeostasis and alleviated cognitive decline in DACI mice. It also mitigated neuronal damage, dendritic degeneration, and synaptic damage, while restoring colonic barrier integrity and ameliorating gut microbiome imbalances, insulin resistance, and lipid imbalance. Additionally, S9P regulated metabolite profiles and the PI3K/AKT/mTOR signaling pathways, and reduced astrocyte activation and neuroinflammatory responses in the hippocampus of HFD-induced DACI mice.

CONCLUSION: S9P had a protective effect against HFD-induced diabetic cognitive impairment closely related to the modulation of the gut-brain axis, suggesting that S9P has the potential to become a new therapeutic approach for DACI.},
}

Animals
*Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome/drug effects/physiology
Mice
*Cognitive Dysfunction/etiology/prevention & control
Male
Mice, Inbred C57BL
*Diabetes Mellitus, Experimental/complications
*Stearic Acids/pharmacology/therapeutic use
*Diabetes Mellitus, Type 2/complications
Blood Glucose/drug effects/metabolism

@article {pmid40325598,
year = {2025},
author = {Nasrah, R and Kanbalian, M and Van Der Borch, C and Dewar, K and Chevalier, S and Jagoe, RT},
title = {Stool Microbiome Features and Weight Change Response to Treatment for cancer cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {3},
pages = {e13816},
doi = {10.1002/jcsm.13816},
pmid = {40325598},
issn = {2190-6009},
support = {//Lady Davis Institute Clinical Research Pilot Project (CliPP), Jewish General Hospital/ ; //Peter Brojde Lung Cancer Centre and the Backler Foundation, Jewish General Hospital Foundation/ ; },
mesh = {Humans ; *Cachexia/etiology/therapy ; Female ; Male ; *Feces/microbiology ; *Neoplasms/complications ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Weight Loss ; },
abstract = {BACKGROUND AND AIMS: Cancer cachexia is characterised by significant weight loss and muscle wasting that adversely affects patient outcomes. Nutritional interventions in cancer cachexia leads to improved outcomes, including improved weight change. However, there are wide variations in weight response to dietary interventions. Thus, it remains difficult to predict response to a given increase in dietary intake at an individual patient level. This study aimed to identify gut microbiome features that could serve as potential predictive biomarkers for response to individualized dietary intervention in patients with cancer cachexia attending the McGill Cancer Nutrition-Rehabilitation Program at the Jewish General Hospital (CNR-JGH).

METHODS: Participants were recruited from CNR-JGH clinic. Interventions included individualized nutritional counselling by a registered dietitian, to increase energy and protein intake to meet recommended levels. Stool DNA samples were collected at baseline (V1) and visit 2 (V2), and gut microbiome profiles were analysed to assess microbial diversity and identify differentially abundant genera in patients who lost weight (WL, N = 8) vs. maintained/gained weight (WSG, N = 29) at subsequent CNR-JGH clinic visits.

RESULTS: Greater alpha-diversity and higher Lachnospira genus abundance at baseline predicted higher likelihood that patients would have good response to CNR-JGH intervention (WSG at V2). Though predictors of poor response to nutritional intervention (WL at V2) were not identified, subjects in the WL group exhibited lower alpha-diversity and greater microbial population instability after CNR-JGH interventions.

CONCLUSIONS: In this cohort of patients with cancer-related weight loss attending a cancer cachexia clinic, certain gut microbiome features were associated with response to dietary interventions. Patients who lost weight after CNR-JGH intervention also developed a less diverse and less stable gut microbiome. Lachnospira genus abundance is a potential predictor of positive weight change response to dietary intervention as part of multimodal care for cancer cachexia, and further confirmatory studies are warranted. In addition, targeted dietary approaches to maintain diversity and gut microbiome population stability may have a role in improving the response to dietary interventions in cancer cachexia.},
}

Humans
*Cachexia/etiology/therapy
Female
Male
*Feces/microbiology
*Neoplasms/complications
*Gastrointestinal Microbiome
Middle Aged
Aged
Weight Loss

@article {pmid40325481,
year = {2025},
author = {Wanelik, KM and Begon, M and Bradley, JE and Fenn, J and Jackson, JA and Paterson, S},
title = {Superspreaders have lower gut microbial alpha-diversity and distinct gut microbial composition in a natural rodent population.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {42},
pmid = {40325481},
issn = {2524-4671},
support = {NE/L013452/1//Natural Environment Research Council/ ; NE/L013452/1//Natural Environment Research Council/ ; NE/L013452/1//Natural Environment Research Council/ ; NE/L013452/1//Natural Environment Research Council/ ; },
abstract = {The microbiome is well known to drive variation in host states (e.g. behaviour, immunity) that would be expected to modulate the spread of infectious disease-but the role of microbiotal interactions in promoting superspreading is poorly understood. Superspreaders are individuals with a strongly disproportionate contribution to pathogen transmission, and come in two forms. Supershedders transmit infection to more individuals because they shed higher levels of pathogen. Supercontacters transmit infection to more individuals because they have larger numbers of social contacts. We explore associations between the gut microbiota and these two forms of superspreading in a wild rodent model-Bartonella spp. bacteraemia in the field vole (Microtus agrestis). We find evidence that individuals fall into distinct shedding and contacting clusters, and that higher-contacters have lower and more variable gut microbial alpha-diversity than lower-contacters. We also show evidence that both higher-shedders and higher-contacters have distinct gut microbial composition and identify OTUs that are differentially abundant in the gut microbiota of these two classes of individuals when compared to lower-shedders and lower-contacters respectively. We find that the Muribaculaceae are associated with differences in both shedding and contacting, and discuss potential mechanisms by which they may be acting on these host traits.},
}

@article {pmid40325409,
year = {2025},
author = {Herbert, J and Thompson, S and Beckett, AH and Robson, SC},
title = {Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {47},
pmid = {40325409},
issn = {2524-6372},
support = {Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; Expanding Excellence in England (E3)//Research England/ ; },
abstract = {INTRODUCTION: Metagenomics, the genomic analysis of all species present within a mixed population, is an important tool used for the exploration of microbiomes in clinical and environmental microbiology. Whilst the development of next-generation sequencing, and more recently third generation long-read approaches such as nanopore sequencing, have greatly advanced the study of metagenomics, recovery of unbiased material from microbial populations remains challenging. One promising advancement in genomic sequencing from Oxford Nanopore Technologies (ONT) is adaptive sampling, which enables real-time enrichment or depletion of target sequences. As sequencing technologies continue to develop, and advances such as adaptive sampling become common techniques within the microbiological toolkit, it is essential to evaluate the benefits of such advancements to metagenomic studies, and the impact of methodological choices on research outcomes.

AIM AND METHODS: Given the rapid development of sequencing tools and chemistry, this study aimed to demonstrate the impacts of choice of DNA extraction kit and sequencing chemistry on downstream metagenomic analyses. We first explored the quality and accuracy of 16S rRNA amplicon sequencing for DNA extracted from the ZymoBIOMICS Microbial Community Standard, using a range of commercially available DNA extraction kits to understand the effects of different kit biases on assessment of microbiome composition. We next compared the quality and accuracy of metagenomic analyses for two nanopore-based ligation chemistry kits with differing levels of base-calling error; the older and more error-prone (~ 97% accuracy) LSK109 chemistry, and newer more accurate (~ 99% accuracy) LSK112 Q20 + chemistry. Finally, we assessed the impact of the nanopore sequencing chemistry version on the output of the novel adaptive sampling approach for real-time enrichment of the genome for the yeast Saccharomyces cerevisiae from the microbial community.

RESULTS: Firstly, DNA extraction kit methodology impacted the composition of the yield, with mechanical bead-beating methodologies providing the least biased picture due to efficient lysis of Gram-positive microbes present in the community standard, with differences in bead-beating methodologies also producing variation in composition. Secondly, whilst use of the Q20 + nanopore sequencing kit chemistry improved the base-calling data quality, the resulting metagenomic assemblies were not significantly improved based on common metrics and assembly statistics. Most importantly, we demonstrated the effective application of adaptive sampling for enriching a low-abundance genome within a metagenomic sample. This resulted in a 5-7-fold increase in target enrichment compared to non-adaptive sequencing, despite a reduction in overall sequencing throughput due to strand-rejection processes. Interestingly, no significant differences in adaptive sampling enrichment efficiency were observed between the older and newer ONT sequencing chemistries, suggesting that adaptive sampling performs consistently across different library preparation kits.

CONCLUSION: Our findings underscore the importance of selecting a DNA extraction methodology that minimises bias to ensure an accurate representation of microbial diversity in metagenomic studies. Additionally, despite the improved base-calling accuracy provided by newer Q20 + sequencing chemistry, we demonstrate that even older ONT sequencing chemistries can achieve reliable metagenomic sequencing results, enabling researchers to confidently use these approaches depending on their specific experimental needs. Critically, we highlight the significant potential of ONT's adaptive sampling technology for targeted enrichment of specific genomes within metagenomic samples. This approach offers broad applicability for enriching target organisms or genetic elements (e.g., pathogens or plasmids) or depleting unwanted DNA (e.g., host DNA) in diverse sample types from environmental and clinical studies. However, researchers should carefully weigh the benefits of adaptive sampling against the potential trade-offs in sequencing throughput, particularly for low-abundance targets, where strand rejection can lead to pore blocking. These results provide valuable guidance for optimising adaptive sampling in metagenomic workflows to achieve specific research objectives.},
}

@article {pmid40325116,
year = {2025},
author = {Yiminniyaze, R and Zhang, Y and Zhu, N and Zhang, X and Wang, J and Li, C and Wumaier, G and Zhou, D and Xia, J and Li, S and Dong, L and Zhang, Y and Zhang, Y and Li, S},
title = {Characterizations of lung cancer microbiome and exploration of potential microbial risk factors for lung cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15683},
pmid = {40325116},
issn = {2045-2322},
support = {82241028//National Clinical Key Specialty Project Foundation/ ; 82270058//National Natural Science Foundation of China/ ; 22Y11900600//Shanghai Year 2022 Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; Male ; Female ; Risk Factors ; *Microbiota/genetics ; Middle Aged ; Aged ; Lung/microbiology/pathology ; High-Throughput Nucleotide Sequencing ; Adult ; Shewanella/isolation & purification/genetics ; },
abstract = {Recent studies have indicated that the lung microbiome may contribute to the development and progression of lung cancer, although the precise mechanisms remain to be fully elucidated. This study sought to delineate the microbial composition within lung cancer tissues and identify potential microbial risk factors. Tissue samples were collected from patients newly diagnosed with pulmonary opacities, and metagenomic next-generation sequencing was employed to analyze these samples. Tissue samples were collected from 130 patients with pulmonary opacities, categorized into lung cancer (50 cases), pulmonary infection (53 cases), and non-infectious pulmonary diseases (27 cases). The non-infectious group served as the primary control. The diversity of the lung microbiome in lung cancer tissues was found to be comparable to that observed in non-infectious benign pulmonary conditions. Specific phyla and genera exhibited increased abundance in lung cancer tissues. Additionally, correlations were established between certain microorganisms and clinical characteristics associated with lung cancer. Multivariate binary logistic regression analysis revealed that age and Shewanella were independent risk factors for lung cancer development. This study suggests that the composition of the lung microbiome differs significantly between individuals with lung cancer and those with benign pulmonary conditions, with certain microbes such as Shewanella potentially serving as risk factors for lung cancer progression.},
}

Humans
*Lung Neoplasms/microbiology/pathology
Male
Female
Risk Factors
*Microbiota/genetics
Middle Aged
Aged
Lung/microbiology/pathology
High-Throughput Nucleotide Sequencing
Adult
Shewanella/isolation & purification/genetics

@article {pmid40324961,
year = {2025},
author = {Ma, L and Ge, Y and Six, N and Choi, SC and Brown, J and Castellanos Garcia, A and Mohamadzadeh, M and Silverman, GJ and Morel, L},
title = {Gut Expansion of a Human Lupus Pathobiont is Associated With Autoantibody Production and T Cell Dysregulation.},
journal = {ACR open rheumatology},
volume = {7},
number = {5},
pages = {e70033},
doi = {10.1002/acr2.70033},
pmid = {40324961},
issn = {2578-5745},
support = {R01 AI143313/AI/NIAID NIH HHS/United States ; },
abstract = {OBJECTIVE: The mechanisms by which the gut microbiome contributes to lupus pathogenesis remain poorly understood. The anaerobe Ruminococcus gnavus (RG) expands in patients with lupus in association with flares. The goal of this study was to determine the mechanisms by which candidate pathobiont lipoglycan-producing RG2 may contribute to autoimmunity and to identify factors promoting its expansion.

METHODS: The consequences of RG colonization or depletion were evaluated in the B6.Sle1.Sle2.Sle3 triple congenic (TC) lupus model by flow cytometry and enzyme-linked immunosorbent assay. RG lysates were tested on Treg cells in vitro. Fecal microbiota transfers evaluated the contribution of the microbiome origin from lupus or control donors and dietary tryptophan. RG1 and RG2 growth and metabolome were evaluated in response to tryptophan in vitro.

RESULTS: Only RG2 stably colonized TC mice, in which it induced autoantibody production and T cell activation. Depletion of anaerobes had the opposite effect, with an increased Treg frequency. RG2 induced Treg apoptosis in cocultures with dendritic cells. RG is present in TC microbiota, from which it is amplified by tryptophan. The combination of TC microbiota and high dietary tryptophan induced autoimmune activation and intestinal inflammation in healthy control mice. Finally, tryptophan enhanced RG2 growth and production of immunomodulatory metabolites.

CONCLUSION: RG2 contributes to autoimmune activation, at least by inducing Treg apoptosis. The expansion of this pathobiont is promoted by host genetic factors and tryptophan metabolism. Thus, targeted RG2 depletion may improve disease outcomes in patients with lupus.},
}

@article {pmid40324646,
year = {2025},
author = {Shen, H and Wang, D and Huang, Y and Yang, Y and Ji, S and Zhu, W and Liu, Q},
title = {2,3,7,8-tetrachlorodibenzofuran modulates intestinal microbiota and tryptophan metabolism in mice.},
journal = {Life sciences},
volume = {373},
number = {},
pages = {123679},
doi = {10.1016/j.lfs.2025.123679},
pmid = {40324646},
issn = {1879-0631},
abstract = {Persistent organic pollutants (POPs) are known to disrupt gut microbiota composition and host metabolism, primarily through dietary exposure. In this study, we investigate the impact of 2,3,7,8-tetrachlorodibenzofuran (TCDF) on gut microbiota and host metabolic processes. RNA-seq analysis revealed that TCDF exposure significantly affected tryptophan metabolism, lipid metabolic pathways, and immune system function. Metagenomic and metabolomic analyses further showed that TCDF reduced the abundance of Mucispirillum schaedleri and levels of two key tryptophan metabolites, indole-3-carboxaldehyde (3-IAld) and Indole acrylic acid (IA). Supplementation with 3-IAld and IA alleviated TCDF-induced liver toxicity in mouse, as evidenced by reduced Cyp1a1 expression, and mitigated intestinal inflammation, reflected by lower pro-inflammatory cytokines (Ifn-γ and Il-1β) in the colon. Additionally, 3-IAld and IA supplementation enhanced intestinal barrier function, as demonstrated by increased Mucin 2 (MUC2) expression in the gut mucosa of mouse. These findings suggest that TCDF exposure disrupts the gut microbiome and host metabolic balance, and highlight the potential therapeutic role of tryptophan-derived metabolites in mitigating environmental pollutant-induced damage.},
}

@article {pmid40324581,
year = {2025},
author = {Vo, Q and Nacionales, DC and McFarland, KN and Gorski, C and Barrios, EL and Park, G and Moldawer, LL and Casadesus, G and Nagpal, R and Efron, PA and Chakrabarty, P},
title = {Temporal impact of sepsis on Alzheimer's disease pathology and neuroinflammation.},
journal = {Progress in neurobiology},
volume = {},
number = {},
pages = {102775},
doi = {10.1016/j.pneurobio.2025.102775},
pmid = {40324581},
issn = {1873-5118},
abstract = {Epidemiological evidence has revealed an associative link between sepsis survivorship and increased risk of dementia, particularly Alzheimer's disease (AD). Paradoxically, population studies show females are less susceptible to sepsis but more vulnerable to post-sepsis dementia. Here, we examined the temporal impacts of sepsis in the context of AD by using an AD-amyloidosis model (TgCRND8) and their wild-type littermates and assessing outcomes at 7 days and 3 months post-sepsis in male and female mice. Following 7-days recovery, the microglia and astrocytes in AD-model mice were largely refractile to the systemic immune stimuli. Notably, the female AD-model mice accumulated higher hippocampal amyloid-beta (Aβ) burden and upregulated AD-type transcriptomic signature at this time. On the other hand, male AD-model mice showed no Aβ changes. At this time, the wild-type post-septic males, but not females, displayed robust astrocytosis, with nominal microgliosis. By 3 months post-sepsis, microgliosis was specifically elevated in wild-type females, indicating a prolonged central immune response. At this time, both male and female AD-model mice showed exacerbated Aβ and anxiety indices. Gene network analysis revealed a stronger immune response in females, while the male response was linked to estrogen receptor (ESR) signaling, with ERα protein upregulated in the brains of post-septic AD-model males. Together, our data highlights a sex-dimorphic temporal response in post-sepsis neuroinflammation, with ESR signaling playing a key role in males, while Aβ burden is affected similarly in both males and females.},
}

@article {pmid40324576,
year = {2025},
author = {Bijle, MN and Pudipeddi, A and Yiu, C},
title = {Effect of direct arginine supplementation on growth of Lacticaseibacillus rhamnosus GG.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105800},
doi = {10.1016/j.jdent.2025.105800},
pmid = {40324576},
issn = {1879-176X},
abstract = {OBJECTIVES: The study aimed to examine the effect of direct arginine (Arg) supplementation on Lacticaseibacillus rhamnosus GG (LRG) growth.

METHODS: The probiotic LRG ATCC 53103 was routinely cultured in MRS broth and adjusted to 10[7] CFU/ml. L-Arg at 0.25% and 0.5% w/v. was directly supplemented to MRS broth containing LRG. Then, LRG with/without supplemented Arg was characterised to determine growth curves for 72 h under a CO2-driven, environment-controlled spectrophotometer. Whereas, end-point McFarland spectrophotometric, metabolic assays (XTT and WST-8), colony forming units (CFU) assessment, live/dead bacterial confocal imaging, and viable DNA quantification were undertaken after 24 h CO2 incubation to determine LRG growth with/without supplemented Arg.

RESULTS: Growth curve analysis revealed similar absorbance profiles with LRG and LRG+0.25% Arg with no overlaps to LRG+0.5% Arg; with a similar trend observed as per end-point McFarland spectrophotometric assessment. The % viability estimated by metabolic assays with LRG and LRG+0.25% Arg was significantly lower than LRG+0.5% Arg (p<0.05). As per CFU assessment, CFU/ml for LRG+0.25% Arg and LRG+0.5% Arg was significantly higher than LRG control (p<0.05). LRG live-dead proportions determined using confocal imaging denote no differences between the groups (p>0.05), with live cell proportions significantly higher than the dead cells (p<0.05). However, LRG cellular density appeared to increase with increasing concentrations of Arg. Additionally, the viable cells quantified with PMA-qPCR significantly increased with increasing concentrations of Arg (p<0.05).

CONCLUSION: Direct supplementation of 0.5% Arg to LRG enhances LRG growth, demonstrating a promising synbiotic potential. CLINICAL SIGNIFICANCE (48 WORDS): Primary caries prevention is initiated at biofilms using biotic strategies that modulate the microbiome matrix to maintain ecological homeostasis. The results of the present study establish a deliverable synbiotic of Arg and probiotic Lacticaseibacillus rhamnosus GG, demonstrating a promising synergism between interventions in the milieu targeted for high caries-risk individuals.},
}

@article {pmid40324150,
year = {2025},
author = {Sudermann, MA and Hua, GKH and Kurth, EG and LeBoldus, JM and Chang, JH and Dung, JKS},
title = {Treatment with the Antimicrobial Product Diallyl Disulfide Is Associated with Major Changes to Soil Microbiota.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-11-24-0366-SC},
pmid = {40324150},
issn = {0031-949X},
abstract = {Natural products derived from Allium spp., such as garlic oil, garlic powder, and diallyl disulfide (DADS), are strong elicitors of sclerotia germination in the fungus Sclerotium cepivorum (syn. Stromatinia cepivora), the causal agent of Allium white rot. However, these compounds can also have broad antimicrobial activity against a wide range of bacteria, oomycetes, and other fungi when they are applied to soil. The objective of this study was to determine the potential impacts that DADS application has on soil microbial communities. DADS was applied to two soil types and incubated under aerobic and anaerobic conditions. Metabarcodes for bacterial, fungal, and oomycete communities were analyzed to identify changes. A significant effect of DADS treatment on the overall compositions of bacterial, fungal, and oomycete communities was observed compared to the mock-treated control. Soil type and incubation conditions did not have a significant effect on soil microbial communities and significant interactions were not observed with DADS treatment in this study. Potential changes in soil microbial communities should be considered when applying DADS to field soils.},
}

@article {pmid40324108,
year = {2025},
author = {Zegeye, FD and Straumfors, A and Lei, P and Graff, P and Samulin Erdem, J and Afanou, AK},
title = {Microbial exposure and diversity in Norwegian shrimp processing plants.},
journal = {Journal of occupational and environmental hygiene},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/15459624.2025.2491488},
pmid = {40324108},
issn = {1545-9632},
abstract = {Seafood processing workers have a high prevalence of respiratory symptoms and occupational asthma, primarily attributed to allergenic protein exposure. However, exposure to airborne microorganisms from raw materials can also contribute to allergic sensitization and other respiratory ailments. This study aimed to assess microbial exposure in shrimp processing plants and identify susceptible work tasks. Full-shift personal air samples were collected from two Norwegian shrimp processing plants across five distinct work processes: thawing, truck driving, cooking-peeling (technician), packing, and flour production. The samples were analyzed for the presence of endotoxin, Toll-Like Receptor (TLR) activation, bacterial and fungal DNA copies, and microbial composition. Endotoxin levels were generally low, with only one sample (98 EU/m[3]) exceeding the recommended occupational exposure limit (OEL). A significant TLR2 activation was observed among thawers, indicating the presence of microbial ligands capable of triggering an immune response. The median bacterial (75 × 10[3] DNA copies/m[3]) and fungal (3,301 × 10[3] DNA copies/m[3]) exposure were highest among the flour production workers, while the lowest bacterial and fungal exposure was among packers (1.5 × 10[3] DNA copies/m[3]) and technicians (337 DNA copies/m[3]), respectively. Several bacterial and fungal species were identified, including ten allergenic and sixteen pathogenic species. Sporobolomyces roseus and Saccharomyces cerevisiae were the two most frequently identified allergenic fungal species. Among the pathogenic bacterial species, Prevotella nigrescens and Roseomonas gilardii were the two most detected species. While the pathogenic species were identified mainly in the packing, truck driving, and flour production work processes, most of the allergenic species were found in all work processes. Altogether, work processes before the cooking of shrimp (thawing and truck driving) had higher endotoxin, bacterial load, and species richness than after cooking, suggesting that these work tasks are susceptible to bacterial exposure and that the cooking process significantly reduces bacterial exposure. By shedding light on microbial exposure and identifying high-exposure work tasks, this study enables the development of targeted interventions and implementation of measures for the prevention of occupational diseases.},
}

@article {pmid40324037,
year = {2025},
author = {Klukoska, M and Ramji, N and Muñoz Bodnar, A and Hu, P and Ye, H and Xie, S and Li, L and Ashe, J and Reichling, T and Wang, J and Milleman, K and Milleman, J},
title = {Clinical effects of stannous fluoride dentifrice on peri-implant mucositis, plaque microbiome, and oxidative stress.},
journal = {American journal of dentistry},
volume = {38},
number = {2},
pages = {59-66},
pmid = {40324037},
issn = {0894-8275},
mesh = {Humans ; *Oxidative Stress/drug effects ; *Tin Fluorides/therapeutic use ; Female ; Male ; *Dental Plaque/microbiology ; Middle Aged ; *Microbiota/drug effects ; Adult ; *Dentifrices/therapeutic use ; *Peri-Implantitis/microbiology/prevention & control/drug therapy ; Periodontal Index ; Biomarkers/analysis ; *Dental Implants/adverse effects ; *Mucositis/drug therapy ; Aged ; Gingival Crevicular Fluid/microbiology ; },
abstract = {PURPOSE: This single-center, single-treatment, 4-week study evaluated the efficacy of a stannous fluoride (SnF2) dentifrice in reducing peri-implant mucositis while assessing changes in biomarkers and the oral microbiome profile.

METHODS: 24 healthy participants 18 years of age or older with osseointegrated implants were included, with 19 participants having mucositis and five without mucositis. The non-mucositis participants served as a reference group for microbiome and biomarker assessments (baseline comparison). All participants used the same 0.454% SnF₂ dentifrice (Crest Pro-Health Sensitive and Enamel Shield) and a soft manual toothbrush twice daily throughout the study. Participants received Modified Gingival Index (MGI) and Gingival Bleeding Index (GBI) assessments at Baseline - Day 1 and at Week 4 - Day 1. Subgingival plaque and peri-implant crevicular fluid (PICF) were collected on Baseline - Day 2 and Week 4 - Day 2 for oxidative stress markers, bacterial endotoxins, proinflammatory cytokines and 16S analysis.

RESULTS: After 4 weeks, participants with mucositis experienced a significant reduction from baseline in MGI and GBI scores (63.4% and 79.3%, respectively) and in the number of bleeding sites (72.5% based on GBI analysis). Microbiome analysis of subgingival plaque showed that mucositis was associated with a higher relative abundance of disease-associated genera (Fusobacterium, Porphyromonas, Treponema, and Prevotella) and a lower relative abundance of commensal genera (Rothia and Actinomyces). Alpha diversity was higher in the mucositis group compared to the non-mucositis group at baseline. By Week 4, the profile of participants with mucositis had shifted to align more closely with that of non-mucositis participants. Participants with mucositis showed significant reduction in biomarkers related to bacterial insult, plaque virulence, oxidative stress, and inflammation. Simulated pathway and process analysis revealed that multiple categories of genes were associated with a state of mucositis, and 4 weeks of use of the experimental dentifrice downregulated several virulence-associated genes.

CLINICAL SIGNIFICANCE: In participants with mucositis, use of a SnF₂ dentifrice for 4 weeks reduced clinical signs and key biomarkers of peri-implant inflammation and shifted the oral microbiome toward a healthier profile, highlighting the utility of SnF₂ dentifrice in the control of peri-implant mucositis.},
}

Humans
*Oxidative Stress/drug effects
*Tin Fluorides/therapeutic use
Female
Male
*Dental Plaque/microbiology
Middle Aged
*Microbiota/drug effects
Adult
*Dentifrices/therapeutic use
*Peri-Implantitis/microbiology/prevention & control/drug therapy
Periodontal Index
Biomarkers/analysis
*Dental Implants/adverse effects
*Mucositis/drug therapy
Aged
Gingival Crevicular Fluid/microbiology

@article {pmid40324006,
year = {2025},
author = {Ye, H and Meehan, D and Timmons, S and O'Toole, PW},
title = {Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00364},
pmid = {40324006},
issn = {1520-5118},
abstract = {A 24 h artificial colon fermentation was performed to assess the effects of a prebiotic MIX and synthetic consortium (S7) on gut microbiota composition and microbial metabolite production in clinically stratified older adults (healthy and frail). Treatments included supplementation of the donor microbiota with a synthetic microbial consortium (S7), a prebiotic mix (MIX), and a combination of MIX and S7 (MIX+S7). The S7 treatment decreased the alpha diversity of long-stay-dwelling donor (LS, "frail") microbiota and increased the relative abundance of S7 taxa at 16 h. MIX alone caused the enrichment of reportedly beneficial genera such as Coprobacillus and Eubacterium in community-dwelling donor (CM, "healthy") microbiota and Citrobacter and Faecalibacterium in LS microbiota. The MIX+S7 treatment sustained higher overall S7 species richness and consortium taxon abundance at 24 h. Both MIX and MIX+S7 treatments enhanced short-chain acid production compared to control. These findings highlight the differential responses of microbiota from distinct elderly health strata to prebiotic and microbial consortia supplementation.},
}

@article {pmid40323787,
year = {2025},
author = {Silva, C and Puthanveetil, P and Oliveira, SD},
title = {Liver Bypass in the Development of Pathogen-associated Pulmonary Vascular Disease: Contribution of Mesocaval and Portosystemic Shunts.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00409.2024},
pmid = {40323787},
issn = {1522-1547},
support = {HL159037//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; CNPq 312051/2023-9//CNPq | Instituto Nacional de Ciência e Tecnologia da Criosfera (INCT da Criosfera)/ ; },
abstract = {Portosystemic and mesocaval shunts are aberrant vascular connections that bypass hepatic filtration, directly linking the portal to the systemic circulation. These shunts, whether congenital or acquired, play a pivotal role in the pathogenesis of schistosomiasis-associated pulmonary hypertension (Sch-PH) by facilitating the dissemination of pathogen-derived eggs and antigens from the guts and mesentery into the lungs. Beyond the translocation of Schistosoma mansoni eggs, emerging evidence implicates that gut-lung microbiome dysbiosis contributes to the development of pulmonary hypertension (PH) in the preclinical animal model of Sch-PH. Sch-PH emerges as a chronic complication of schistosomiasis and evolves silently, progressively increasing the mean pulmonary arterial pressure and vascular resistance, leading to right heart hypertrophy, failure, and significant morbidity and mortality. Chronic schistosomiasis is often linked to the development of portal hypertension, which significantly contributes to the formation of the porto/mesocaval shunt as a compensatory response that can have far-reaching implications on pulmonary vascular physiology. Additionally, portal hypertension compromises the integrity of the intestinal barrier, exacerbating peritoneal and mesenteric inflammation, potentially facilitating microbial and metabolite entrance into the systemic circulation.This article briefly discusses the mechanisms by which porto/mesocaval shunts contribute to PH, especially Group I PH, focusing on the interplay between portosystemic shunting, microbial translocation, and systemic dissemination of pro-inflammatory metabolites.},
}

@article {pmid40323603,
year = {2025},
author = {Chaturvedi, AK and Vogtmann, E and Shi, J and Yano, Y and Blaser, MJ and Bokulich, NA and Caporaso, JG and Gillison, ML and Graubard, BI and Hua, X and Hullings, AG and Kahle, L and Knight, R and Li, S and McLean, J and Purandare, V and Wan, Y and Freedman, ND and Abnet, CC},
title = {Oral Microbiome Profile of the US Population.},
journal = {JAMA network open},
volume = {8},
number = {5},
pages = {e258283},
doi = {10.1001/jamanetworkopen.2025.8283},
pmid = {40323603},
issn = {2574-3805},
mesh = {Humans ; Adult ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; United States/epidemiology ; Cross-Sectional Studies ; *Mouth/microbiology ; Aged ; Young Adult ; Adolescent ; Nutrition Surveys ; RNA, Ribosomal, 16S ; },
abstract = {IMPORTANCE: The oral microbiome likely plays key roles in human health. Yet, population-representative characterizations are lacking.

OBJECTIVE: To characterize the composition, diversity, and correlates of the oral microbiome in US adults.

This cross-sectional study analyzed data from the population-representative National Health and Nutrition Examination Survey (NHANES) from 2009 to 2012. Microbiome data were made publicly available in 2024. NHANES participants were aged 18 to 69 years and provided oral rinse samples in 1 of 2 consecutive NHANES cycles (2009-2010 and 2011-2012).

EXPOSURES: Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics.

MAIN OUTCOMES AND MEASURES: Oral microbiome measures, characterized through 16S ribosomal RNA gene sequencing, included α diversity (observed amplicon sequence variants [ASVs], Faith phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); β diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at phylum level through genus level. Analyses accounted for the NHANES complex sample design.

RESULTS: This study included 8237 US adults aged 18 to 69 years, representing 202 314 000 individuals (102 813 000 men [50.8%]; mean [SD] age, 42.3 [14.4] years; 9.3% self-reported as Mexican American, 12.1% as non-Hispanic Black, 64.7% as non-Hispanic White, 5.9% as other Hispanic, and 8.1% as other non-Hispanic individuals). The oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1219 genera. Five phyla (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria) and 6 genera (Veillonella, Streptococcus, Prevotella 7, Rothia, Actinomyces, and Gemella) were present in nearly all US adults (weighted prevalence, >99%). These genera were the most abundant, accounting for 65.7% of total abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), were similar by sex, significantly lower among non-Hispanic White individuals, and increased with greater body mass index (BMI), alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability as measured by β diversity: R2 = 8.7% (95% CI, 8.4%-9.1%) for unweighted UniFrac, R2 = 7.2% (95% CI, 6.6%-7.7%) for weighted UniFrac, and R2 = 6.3% (95% CI, 3.1%-6.7%) for Bray-Curtis matrices. By contrast, relative abundance of a few genera explained a high percentage of variability in β diversity for weighted UniFrac: Aggregatibacter (R2 = 22.4%; 95% CI, 22.1%-22.8%), Lactococcus (R2 = 21.6%; 95% CI, 20.9%-22.3%), and Haemophilus (R2 = 18.4%; 95% CI, 18.1%-18.8%). Prevalence and relative abundance of numerous genera were associated with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity.

CONCLUSIONS AND RELEVANCE: This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population. This comprehensive characterization provides a contemporary reference standard for future studies.},
}

Humans
Adult
Male
Female
Middle Aged
*Microbiota/genetics
United States/epidemiology
Cross-Sectional Studies
*Mouth/microbiology
Aged
Young Adult
Adolescent
Nutrition Surveys
RNA, Ribosomal, 16S

@article {pmid40323507,
year = {2025},
author = {Wadan, AS and El-Aziz, MKA and Ellakwa, DE},
title = {The microbiota-gut-brain-axis theory: role of gut microbiota modulators (GMMs) in gastrointestinal, neurological, and mental health disorders.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {40323507},
issn = {1432-1912},
abstract = {The modulation of gut microbiota presents promising therapeutic possibilities for various health conditions, ranging from gastrointestinal infections to neurodegenerative and mental health disorders. Among the available interventions, gut microbiota modulators (GMMs) such as probiotics and prebiotics have demonstrated significant potential in infection prevention and neuroprotection. Despite these encouraging findings, the clinical application of GMMs remains challenging due to safety concerns and inconsistent effectiveness across diverse patient populations. These factors create substantial barriers to the widespread adoption of microbiota-based therapies in clinical practice. To overcome these challenges and fully leverage the therapeutic potential of microbiota modulation, this review explores the feasibility of repurposing GMMs for managing multiple health disorders. A broad spectrum of microbiota-targeted strategies is examined, including dietary modifications, fecal microbiota transplantation, bacteriophage therapy, microbiome engineering, and immune system modulation. A particularly innovative approach involves integrating GMMs with pharmaceutical delivery systems to enhance therapeutic efficacy while mitigating potential adverse effects. This integrative strategy underscores the pivotal role of the gut microbiome in health and disease, supporting the development of precision medicine tailored to individual patient needs. By combining GMMs with targeted delivery mechanisms, this approach not only improves treatment effectiveness but also addresses critical concerns regarding safety and patient variability. Furthermore, this review outlines future research directions within the rapidly evolving field of microbiota modulation, emphasizing the necessity of comprehensive clinical trials and long-term safety evaluations. By critically assessing both the challenges and opportunities associated with microbiota-based interventions, this study provides a strategic framework for translating experimental research into viable clinical applications. A holistic approach to gut microbiota modulation has the potential to redefine treatment paradigms, offering personalized therapeutic strategies for a wide range of disorders and advancing the broader field of precision medicine.},
}

@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}

Humans
*Dysbiosis/microbiology
*Mycobiome
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Inflammation/microbiology
*Gastrointestinal Neoplasms/microbiology
Fungi/pathogenicity
Animals

@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid40323426,
year = {2025},
author = {Atuk Kahraman, T and Yılmaz, M and Aslan, K and Canatan, H and Kara, A and Nalbantoglu, OU and Gundogdu, A and Eken, A},
title = {Lycopene Supplemented Mediterranean Diet Ameliorates Experimental Autoimmune Encephalomyelitis (EAE) in Mice and Changes Intestinal Microbiome.},
journal = {Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology},
volume = {20},
number = {1},
pages = {50},
pmid = {40323426},
issn = {1557-1904},
mesh = {Animals ; *Lycopene/administration & dosage/pharmacology ; *Encephalomyelitis, Autoimmune, Experimental/diet therapy/immunology ; Female ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects/physiology ; *Diet, Mediterranean ; *Dietary Supplements ; },
abstract = {This study aimed to determine the effects of the Mediterranean diet (MD) and lycopene on the development of EAE and on inflammatory markers. In the 43-day study, 72 female C57BL/6 mice were randomly divided into eight groups according to whether they were EAE or naive (control) mice, fed a Western diet or a MD, and whether they received lycopene. During the study, mice were fed ad libitum, and lycopene groups were given 10 mg/kg/day lycopene per mouse every other day for 28 days in oral gavage. The mice were scored for EAE, sacrificed and their spleen, lymph nodes, and spinal cords were removed. We observed slightly delayed EAE onset in the MD-Lyc group compared to the others, and the EAE clinical scores were also lower than in the other groups. T-cell counts in the spleen and lymph nodes of the MD-Lyc group were significantly lower than in other groups. The production of IFN-γ and IL-22 was higher than in the other groups. IL-17 A cytokine produced in the spleen was lower in the MD-Lyc group than in the other groups. In addition, the highest myelination score was seen in the MD-Lyc group. MD-Lyc group also had a unique microbiome profile compared with the remaining groups. In summary, MD and lycopene administration positively impacted EAE scores and myelination. However, more comprehensive studies at the in vitro and in vivo levels are needed to reveal the effect of this intervention on cell numbers in the CNS.},
}

Animals
*Lycopene/administration & dosage/pharmacology
*Encephalomyelitis, Autoimmune, Experimental/diet therapy/immunology
Female
Mice
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects/physiology
*Diet, Mediterranean
*Dietary Supplements

@article {pmid40323322,
year = {2025},
author = {Chen, X and Sui, Y and Gu, J and Wang, L and Sun, N},
title = {The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf042},
pmid = {40323322},
issn = {2210-3244},
abstract = {The rise in infertility rates has prompted research into the impact of vaginal microbiota on female fertility and assisted reproduction technology (ART) success. Our study compares the vaginal microbiome of fertile and infertile women and explores its influence on ART outcomes. We analyzed vaginal secretions from 194 infertile women and 100 healthy controls at Shanghai Changzheng Hospital using polymerase chain reaction (PCR) to amplify the 16S rRNA V3-V4 region. A machine learning model predicted infertility based on genus abundances, and the PICRUSt algorithm predicted metabolic pathways related to infertility and ART outcome. The results showed women with infertility exhibited a significantly different vaginal microbial composition compared to healthy women, with the infertility group showing higher microbial diversity. Burkholderia, Pseudomonas, and Prevotella levels were significantly elevated in the vaginal microbiota of the infertility group, while Bifidobacterium and Lactobacillus abundances were reduced. Recurrent implantation failure (RIF) within the infertile population showed even higher diversity of vaginal microbiota, with specific genera such as Mobiluncus, Peptoniphilus, Prevotella, and Varibaculum being more abundant. Eleven metabolic pathways were associated with RIF and infertility, with Prevotella demonstrating stronger correlations. The present study provides insights into the differences in vaginal microbiome between healthy and infertile women, offering a new understanding of how vaginal microbiota may impact infertility and ART outcomes. Our findings underscore the significance of specific microbial taxa in women with RIF, suggesting avenues for targeted interventions to enhance embryo transplantation success rates.},
}

@article {pmid40323242,
year = {2025},
author = {Ofori-Kwafo, A and Sigdel, I and Al Mamun, E and Zubcevic, J and Tang, Y},
title = {Gut-on-a-chip platforms: Bridging in vitro and in vivo models for advanced gastrointestinal research.},
journal = {Physiological reports},
volume = {13},
number = {9},
pages = {e70356},
doi = {10.14814/phy2.70356},
pmid = {40323242},
issn = {2051-817X},
mesh = {Humans ; *Lab-On-A-Chip Devices ; *Gastrointestinal Tract/physiology ; Animals ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; },
abstract = {The gastrointestinal (GI) tract plays a critical role in nutrient absorption, immune responses, and overall health. Traditional models such as two-dimensional cell cultures have provided valuable insights but fail to replicate the dynamic and complex microenvironment of the human gut. Gut-on-a-chip platforms, which incorporate cells located in the gut into microfluidic devices that simulate peristaltic motion and fluid flow, represent a significant advancement in modeling GI physiology and diseases. This review discusses the evolution of gut-on-a-chip technology, from simple cellular mono-cultures models to more sophisticated systems incorporating bi-cultures and tri-cultures that enable studies of drug metabolism, disease modeling, and gut-microbiome interactions. Although challenges remain, including maintaining long-term cell viability and replicating immune responses, these platforms hold great potential for advancing personalized medicine and improving drug discovery efforts targeting gastrointestinal disorders.},
}

Humans
*Lab-On-A-Chip Devices
*Gastrointestinal Tract/physiology
Animals
Gastrointestinal Diseases
Gastrointestinal Microbiome