@article {pmid40914698,
year = {2025},
author = {Wang, S and Peng, G and Abudouwanli, A and Yang, M and Sun, Q and Zhao, W and Ikeda, A and Tan, Y and Ma, L and Ogawa, H and Okumura, K and Niyonsaba, F},
title = {The interaction between the skin microbiome and antimicrobial peptides within the epidermal immune microenvironment: Bridging insights into atopic dermatitis.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2025.08.002},
pmid = {40914698},
issn = {1440-1592},
abstract = {The epidermal immune microenvironment is a multifaceted system in which the interplay between the skin microbiome and antimicrobial peptides plays a pivotal role in sustaining skin homeostasis and preventing dysbiosis. Disruption of these interactions can lead to inflammatory skin conditions such as atopic dermatitis. This review aims to explore the complex mechanisms by which antimicrobial peptides and the skin microbiome communicate within the epidermal immune microenvironment, emphasizing causal dynamics and the dual role of antimicrobial peptides. This analysis opens new avenues for targeted interventions, including antimicrobial peptide modulation and microbiome-based therapies, to restore skin health and mitigate inflammatory skin disorders.},
}

@article {pmid40914516,
year = {2025},
author = {Hiol, A and Veiga, P},
title = {From the Lab to the Plate: How Gut Microbiome Science is Reshaping Our Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.032},
pmid = {40914516},
issn = {1541-6100},
abstract = {This review explores the century-long trajectory of gut microbiome research and its contribution to shaping our modern diet. It further highlights the transformative potential of current discoveries to revolutionize future dietary habits and nutritional practices. From the pioneering work of E. Metchnikoff in the early 20th century, which led to the widespread adoption of yoghurt in many Western countries, to the emergence of probiotics and prebiotics, the microbiota has become a key determinant in human health and nutrition. Current developments provide new perspectives on the future, such as next-generation probiotics and prebiotics, dietary recommendations adapted to the specific needs of the microbiota, and precision nutrition that considers individual microbiota variability.},
}

@article {pmid40914513,
year = {2025},
author = {Bartsch, M and Vital, M and Woltemate, S and Bouwman, FG and Berkemeyer, SB and Hahn, A and Müller, M},
title = {Microbiota-Dependent Fiber Responses: A Proof-of-Concept Study on Short-chain Fatty Acid Production in Prevotella- and Bacteroides-Dominated Healthy Individuals.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.034},
pmid = {40914513},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary fiber supports metabolic health via microbial fermentation, producing short-chain fatty acids (SCFAs). However, metabolic responses to fiber vary between individuals, potentially due to differences in gut microbiota composition. The Prevotella-to-Bacteroides (P/B) ratio has emerged as a potential biomarker for fiber responsiveness.

OBJECTIVE: This study examined how stratified fiber supplementation affects microbial and metabolic outcomes in individuals with Prevotella- or Bacteroides-dominated microbiota.

METHODS: In this single-blinded, randomized cross-over study, 23 healthy adults were classified as P-type (≥10% Prevotella) or B-type (≥10% Bacteroides) via 16S rRNA sequencing. Participants consumed 15 g/day of arabinoxylan (AX), inulin (INU), or placebo (PLA) for one week each, with 2-week washouts. After each phase, fasting and postprandial plasma SCFAs, branched-chain fatty acids (BCFAs), breath hydrogen, glucose, insulin, PYY, cholesterol, appetite ratings, and fecal microbiota were assessed. Data were analyzed using repeated measures ANOVA, Friedman test, and multivariate microbiome analysis.

RESULTS: In P-types, AX increased fasting propionate vs. PLA (p = 0.04). In B-types, AX increased fasting propionate vs. INU (p = 0.02) and tended to elevate postprandial propionate vs. PLA in the first 60 minutes after breakfast (p = 0.05). AX also increased postprandial acetate vs. PLA in B-types (p = 0.04). INU reduced fasting BCFAs in B-types (p < 0.05) but did not increase SCFAs. Breath hydrogen varied widely in B-types after INU but not in P-types. Neither fiber affected glucose, insulin, or PYY. AX reduced appetite ratings in P-types (p < 0.05). INU increased Anaerostipes and Bifidobacterium and reduced Phocaeicola in both groups (q < 0.25). AX increased Fusicatenibacter in B-types (q = 0.18) and Paraprevotella in P-types (q = 0.17).

CONCLUSIONS: B-types exhibited fiber-specific shifts in SCFA and BCFA metabolism and breath hydrogen, whereas P-types displayed a more limited overall response, with fewer metabolic and microbial parameter affected. These findings highlight the complexity of diet-microbiota interactions and support the potential relevance for microbiota-based nutrition strategies. German Register of Clinical Studies (DRKS00028898).},
}

@article {pmid40914511,
year = {2025},
author = {Li-Hua, P and Bajinka, O},
title = {Processed Meat Health Risks: Pathways and Dietary Solutions.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.030},
pmid = {40914511},
issn = {1541-6100},
abstract = {BACKGROUND: Red and processed meat consumption is extensively linked to chronic disease risk in observational studies, with robust meta-analyses demonstrating significant positive associations for colorectal, breast, endometrial, and lung cancers, type 2 diabetes (T2DM), cardiovascular disease (CVD), and all-cause mortality. Dose-response relationships indicate elevated risks even at moderate intakes. Moreover, processed meats consistently show stronger detrimental effects than unprocessed red meats. Biological mechanisms include carcinogen formation, pro-inflammatory effects, gut microbiome dysbiosis, and impacts on lipid metabolism and insulin resistance. However, evidence exhibits complexities, including inconsistent RCT findings on short-term biomarkers, weaker associations for unprocessed red meat in some outcomes, and significant modulation by overall diet, lifestyle, and genetic factors.

OBJECTIVE: This review synthesizes epidemiological evidence on red and processed meat consumption and chronic disease risk, elucidates the multifaceted biological mechanisms underlying these associations including carcinogenesis, cardiometabolic pathways, and microbiome interactions, and critically evaluates evaluating contextual modifiers such as processing methods including the use of 'natural' nitrate sources, cooking techniques, and dietary patterns, and lifestyle factors. It also identifies key research gaps and limitations to inform future studies and evidence-based dietary guidance.

CONCLUSION: High processed meat intake is robustly associated with increased risks of multiple chronic diseases and mortality via mechanisms involving mutagenic compounds, heme iron, TMAO, saturated fats, and gut dysbiosis. Unprocessed red meat shows weaker, less consistent links. Crucially, replacing red/processed meats with plant proteins, poultry, or fish reduces disease risk through beneficial mechanisms. Risk is modified by processing, cooking methods, overall dietary patterns, and physical activity. Public health recommendations should prioritize minimizing processed meat, moderating unprocessed red meat, and emphasizing healthier substitutions within balanced diets. Future research must address causality, mechanistic specificity, population diversity, and integrated health-environmental assessments.},
}

@article {pmid40914481,
year = {2025},
author = {Nie, C and Qi, Y and Wang, T and Shan, Y and Xie, C and Jiang, Z and Ke, Z and Zhang, L and Du, S and Xiong, H and Yao, J},
title = {Nanodrug-based therapeutic interventions for tumor-associated microbiota modulation.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {114196},
doi = {10.1016/j.jconrel.2025.114196},
pmid = {40914481},
issn = {1873-4995},
abstract = {The tumor microenvironment (TME) is a complex and dynamic ecosystem that significantly influences tumor progression, immune modulation, and therapeutic response. A key component of the TME is the tumor-associated microbiota, which has emerged as an important player in cancer biology, affecting tumor metastasis, immune evasion, and resistance to treatments. The recent advent of high-throughput sequencing technologies has revolutionized our understanding of the microbiome, revealing distinct microbial communities across various tumor types. These microbes engage in bidirectional interactions with tumor cells and the immune system, shaping the inflammatory milieu and immune responses that ultimately influence tumor outcomes. Consequently, manipulating tumor-associated microbiota has become an exciting strategy to enhance cancer therapy. By harnessing tailored physicochemical properties and structural design, nanotechnology-based drug platforms can precisely remove tumor-associated microbiota and microbial communities within the TME, while simultaneously delivering antimicrobials, immunomodulators, or probiotics to boost immune responses and overcome resistance. However, the complexity and heterogeneity of the microbiome and TME present significant challenges in the development of universal therapeutic approaches. This review highlights the role of tumor-associated microbiota in tumor biology, the mechanisms by which microbiota influence tumor progression and therapeutic resistance, and the potential of nanodrug-based strategies for microbiome modulation in cancer treatment. By elucidating these mechanisms, we aim to provide insights into the therapeutic potential of microbiome-targeted therapies for precision oncology.},
}

@article {pmid40914466,
year = {2025},
author = {Luo, HY and Cao, LM and Zhou, K and Xiao, Y and Li, ZZ and Liu, B and Bu, LL},
title = {Microbiome unlocks cancer immunotherapeutic potential: state of the art and future.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.08.001},
pmid = {40914466},
issn = {1096-3650},
abstract = {Immunotherapy has overturned the traditional perception of cancer treatment and brought new vitality to the field of oncology, but it still has unresolved problems such as a low response rate and severe side effects. The microbiome has been found to be involved in tumorigenesis, progression, metastasis and immunity modulation. Especially in immunity, the microbiome plays a key role through delicate mechanisms that regulate the immune response not only from the whole body to the local tumor microenvironment but also from innate to adaptive immunity. We summarize the specific relationship between tumor-associated microbiomes at different sites (gut, oral, intratumoral) and cancer immunity, especially pay attention to the microbiome besides the gut. The microbiome-based immunotherapy has been innovatively categorized as follows. ⅰ) Bacteria-based immunotherapy and engineered bacteria as a new strategy to be used in immunotherapy. ⅱ) Microbiome combined with immunotherapy to improve efficacy and mitigate side effects. Finally, we conclude with insights into the shortcomings and future directions of microbiome in immunotherapy.},
}

@article {pmid40914399,
year = {2025},
author = {Ji, X and Zhu, K and Zhang, L},
title = {Biocarrier-driven enhancement of caproate production via microbial chain elongation: Linking metabolic redirection and microbiome assembly.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133272},
doi = {10.1016/j.biortech.2025.133272},
pmid = {40914399},
issn = {1873-2976},
abstract = {This study investigated the effects of five representative biocarriers-biochar (BC), activated carbon (AC), nano-magnetite (NM), zero-valent iron (ZVI), and polyurethane sponge (PUS)-on chain elongation (CE) from ethanol/acetate in anaerobic systems. All carriers enhanced CE to varying extents. BC and NM significantly increased caproate yields (6032.6 and 5996.6 mg/L) and shortened lag phases (6.22 and 7.18 days) compared with Control (2226.6 mg/L, 11.61 days). In the second cycle, carbon selectivity rose to 58.9 % and 58.0 % with AC and BC, respectively, versus 18.9 % in Control. Biocarrier addition enriched chain-elongating syntrophs, increased community diversity, and elevated predicted fatty acid biosynthesis gene abundance, shifting metabolism toward caproate over reduced byproducts. These findings demonstrate that carbonaceous biocarriers simultaneously alleviate product inhibition, restructure microbial networks, and reprogram metabolic pathways, providing a mechanistic basis for selective biocarrier use in microbiome engineering for medium-chain fatty acid production.},
}

@article {pmid40914285,
year = {2025},
author = {Sood, R and Kilpatrick, LA and Keefer, LA and Church, A},
title = {Biopsychosocial and Environmental Factors that Impact Brain-Gut-Microbiome Interactions in Obesity.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2025.07.045},
pmid = {40914285},
issn = {1542-7714},
abstract = {BACKGROUND: Despite significant advances in the understanding of the pathogenesis of obesity and influencing factors, its prevalence continues to increase at an alarming rate. Social determinants of health (SDOH) encompass a broad range of psychosocial and environmental factors, including economic stability, education, access to healthcare, social support, isolation, neighborhood disadvantage, discrimination, early life adversity, and stress, all of which have been recognized to significantly increase the risk of obesity.

AIM: This review aims to elucidate the intricate relationship between SDOH and biological mechanisms related to the brain-gut-microbiome (BGM) system that lead to altered eating behaviors and obesity.

METHODS: We conducted a systematic review of the current literature to discuss how SDOH contribute to the development, progression, and management of obesity; and on the BGM mechanisms involved in the influence of SDOH on obesity.

RESULTS: The BGM mediates the relationship between SDOH and obesity via orexogenic peptides, inflammatory markers, and neuroactive metabolites that affect ingestion-related decision-making and mood. Dysregulations in the BGM system as a result of environmental stressors can contribute to physiological changes in the gut microbial composition, hypothalamic-pituitary-adrenal axis signaling, and structural changes in the reward network, collectively leading to an increased drive toward the consumption of calorie-dense foods.

CONCLUSIONS: By recognizing and addressing the impact of various SDOH on BGM interactions, healthcare providers can provide a more equitable and personalized approach that will enhance treatment adherence and the quality of life for individuals with obesity.},
}

@article {pmid40914165,
year = {2025},
author = {Anani, H and Destras, G and Bulteau, S and Castain, L and Semanas, Q and Burfin, G and Petrier, M and Martin, FP and Poulain, C and Dickson, RP and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102289},
doi = {10.1016/j.xcrm.2025.102289},
pmid = {40914165},
issn = {2666-3791},
abstract = {Hospital-acquired pneumonia (HAP) is one of the most common nosocomial infections, leading to significant morbidity and mortality in critically ill patients. HAP is previously associated with dysbiosis of the microbiota. However, the composition of the lung virome and its role in HAP pathogenesis remain unclear. Here, we longitudinally analyze the endotracheal virome in 87 critically ill patients, including 48 with HAP. Within the virome dominated by Caudoviricetes, a decrease in viral beta-diversity toward a bacteriophage-dominated signature and a distinct viral-bacterial interactome is observed 5-4 days before HAP onset. Lung virome composition, viral convergence before HAP onset, and conservation of 18% of the bacteriophage signature are validated in an external cohort of 40 patients. In silico causal inference further identifies bacteriophages associated with Streptococcus and Prevotella as a key regulator of HAP onset. These findings suggest an uncovered pathophysiological mechanism of HAP with virome involvement in lung microbiota dysbiosis. The discovery and validation studies are registered at ClinicalTrials.gov (NCT02003196 and NCT04793568).},
}

@article {pmid40914155,
year = {2025},
author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR},
title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.08.005},
pmid = {40914155},
issn = {1932-7420},
abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.},
}

@article {pmid40914111,
year = {2025},
author = {Park, MK and Jang, H and Park, YJ and Park, TH and Kim, C and Kim, HJ and Lee, SE and Park, HJ and Lee, S and Lee, YM and Shin, JH},
title = {Biologically safe restoration of heavy metal-contaminated soils through plant-microbe synergy.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180404},
doi = {10.1016/j.scitotenv.2025.180404},
pmid = {40914111},
issn = {1879-1026},
abstract = {Abandoned mines have created extensive idle areas contaminated with heavy metals (HMs). Conventional remediation methods are often costly, environmentally disruptive, and pose risks to human health. As a sustainable alternative, a biological approach utilizing metal-tolerant plant growth-promoting bacteria (mPGPBs) was employed to remediate HM-contaminated soils and assess their biological safety. Five mPGPB strains-Pseudarthrobacter sp., Pseudomonas sp., and Agrobacterium sp.-were isolated from contaminated mine soils and screened for metal tolerance and plant growth-promoting capabilities. Inoculation of Solanum nigrum L. with Agrobacterium sp. NIBRBAC000502774 proved most effective for phytoremediation, significantly increasing total dry biomass by 139% (from 0.158 ± 0.039 g to 0.378 ± 0.059 g/plant) and showing the highest HM bioconcentration (1.4- to 13.2-fold) compared to uninoculated controls. In subsequent in vivo biosafety assays, soil remediated with Pseudarthrobacter sp. NIBRBAC000502770 was the most effective at attenuating HM-induced hepatotoxicity in mice, as evidenced by normalized liver enzyme levels and reduced apoptosis. Furthermore, mPGPB treatment shifted from HM-tolerant taxa toward a dominance of Proteobacteria and Actinobacteria, and functional predictions indicated enhanced biosynthesis of secondary metabolites. Our findings suggest that specific mPGPBs offer a promising biological approach for restoring idle areas by enhancing the growth and HM uptake of hyperaccumulator plants, thereby reducing environmental HM toxicity and associated health risk. This method also demonstrates biological safety, making it a valuable alternative to conventional remediation techniques for environmental restoration, with the potential to reduce the incidence of diseases associated with HM exposure.},
}

@article {pmid40914087,
year = {2025},
author = {Zhang, Y and Li, X and Chen, L and Terzaghi, W and Zheng, X and Zhang, J and Zhang, H and Zhang, H and Cao, X and Li, Y and Yang, L and Song, K and Lv, W},
title = {Synergistic enhancement effect of straw-earthworms in the reduction of sulfamethoxazole and antibiotic resistance genes.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119001},
doi = {10.1016/j.ecoenv.2025.119001},
pmid = {40914087},
issn = {1090-2414},
abstract = {Soil antibiotic pollution is a global concern. It has been confirmed that straw or earthworm can enhance microbial degradation of antibiotics in soil. However, in the C/N transformation processes of soil ecosystems, straw and earthworms are closely interconnected. Whether their interaction can further enhance microbial degradation of antibiotic pollution and the underlying mechanisms remain to be explored. This study conducted a 90 days co-incubation experiment with four treatments: straw + earthworms + sulfamethoxazole (RS-EW-SMX), straw + SMX (RS-SMX), earthworms + SMX (EW-SMX), and SMX alone (SMX). Residual SMX, its degradation intermediates, and microbial communities were monitored at multiple timepoints. Results indicated an exponential decline in SMX degradation rates across treatments. By day 90, SMX was nearly completely degraded in all treatment groups. However, the combined effect of straw and earthworms significantly enhanced the degradation efficiency of SMX. During the rapid degradation phase, SMX in above four treatments decreased from 20.0 mg kg[-1] to 0.93, 1.88, 5.26 and 7.02 mg kg[-1], respectively at day 10. Furthermore, the RS-EW-SMX treatment promoted SMX transformation into low-molecular-weight intermediates and increased the relative abundance of SMX-degrading bacteria by 1.35, 2.01, and 2.17-fold compared to RS-SMX, EW-SMX, and SMX, respectively. SMX degradation efficiency exhibited a strong positive linear correlation with the relative abundance of degrading bacteria across all treatments (R[2] = 0.961). Concurrently, analysis revealed that straw presence facilitated the targeted enrichment of SMX-degrading bacteria within the earthworm gut, concomitant with a reduction in associated antibiotic resistance genes (ARGs). This synergistic interaction between straw and earthworms, mediated through the gut microbiome and carbon utilization, constitutes a primary mechanism underpinning the accelerated SMX degradation observed. These findings reveal a novel macrofauna-plant residues interaction mechanism for improved in situ antibiotic bioremediation, providing practical solutions for soil pollution mitigation.},
}

@article {pmid40914074,
year = {2025},
author = {Topkan, E and Somay, E and Selek, U},
title = {Oral microbiome in head and neck squamous cell cancers: association or causation?.},
journal = {Oral oncology},
volume = {169},
number = {},
pages = {107650},
doi = {10.1016/j.oraloncology.2025.107650},
pmid = {40914074},
issn = {1879-0593},
}

@article {pmid40913888,
year = {2025},
author = {Chen, J and Zhao, H and Méndez-Sánchez, N and Qi, X},
title = {Probiotics for the Management of Liver Cirrhosis and Its Complications.},
journal = {Archives of medical research},
volume = {56},
number = {8},
pages = {103304},
doi = {10.1016/j.arcmed.2025.103304},
pmid = {40913888},
issn = {1873-5487},
abstract = {Cirrhosis is the terminal stage of various chronic liver diseases, and its decompensated stage is mainly characterized by serious complications, such as hepatic encephalopathy, ascites, spontaneous bacterial peritonitis, and gastrointestinal bleeding. Gut microbial dysbiosis is prevalent in patients with cirrhosis. Considering the bidirectional regulation of the gut-liver axis, dysbiosis is closely related to the development and progression of liver cirrhosis. Probiotics, which modulate the gut microbiome, have received significant attention for managing cirrhosis and its complications. Through a review of relevant literature, we have provided a comprehensive summary of the potential efficacy of probiotics in treating cirrhosis and its complications, providing new insights into targeting the gut microbiome.},
}

@article {pmid40913864,
year = {2025},
author = {Xiang, X and Zhu, Y and Wang, T and Zhu, J and Ding, P and Cheng, K and Ming, Y},
title = {Gut microbiota and metabolites related intra-patient variability of tacrolimus pharmacokinetics predicted adverse one-year outcomes following kidney transplantation.},
journal = {International immunopharmacology},
volume = {165},
number = {},
pages = {115506},
doi = {10.1016/j.intimp.2025.115506},
pmid = {40913864},
issn = {1878-1705},
abstract = {Kidney transplantation (KT) is an effective treatment for end-stage renal disease, with over 90 % of recipients requiring lifelong tacrolimus (Tac). However, The Tac pharmacokinetics exhibit high intra-patient variability (IPV), posing significant challenges. This study included 102 KT recipients at our center from October 2022 to December 2023. Patients were stratified into high- and low-IPV groups based on the median coefficient of variation of the the Tac trough concentration-to-dose ratio during the first post-transplant month. Fecal samples were collected for 16S rRNA sequencing and untargeted metabolomics analysis, while clinical outcomes within the first year were assessed for associations with the Tac IPV. Microbiome analysis revealed significant beta diversity differences (p = 0.0451) and 19 differential taxa, including g__Clostridia_vadinBB60_group enriched in high-IPV patients and g__Clostridia_UCG_014 in the low-IPV group. Metabolomics identified 1298 differential metabolites, with 729 enriched in high-IPV patients. Network analysis highlighted cholesterol and unsaturated fatty acid biosynthesis as central pathways, while both microbial functional predictions and metabolic enrichment analyses emphasized bile secretion. A random forest model validated the classification potential of these biomarkers, and associations between differential taxa and metabolites were observed. Clinical correlation analysis indicated the high Tac IPV as an independent protective factor against post-transplant hyperuricemia but a positive predictor of new-onset diabetes. This study is the first to link the Tac IPV, gut microbiota, metabolism, and one-year outcomes, offering novel insights into personalized care and the mechanisms underlying the Tac IPV.},
}

@article {pmid40913776,
year = {2025},
author = {Reich, K and Trettel, N and Reich, JLK and Sorbe, C and Bickert, T and Hartmann, J and Harder, I and Gerdes, S and Weidinger, S},
title = {Effects of a gel containing the defined microalgae extract Spiralin® on the skin microbiome and clinical activity in atopic dermatitis - a double-blind, intraindividual vehicle-controlled proof-of-concept study.},
journal = {Skin pharmacology and physiology},
volume = {},
number = {},
pages = {1-10},
doi = {10.1159/000547835},
pmid = {40913776},
issn = {1660-5535},
abstract = {INTRODUCTION: Changes in the skin microbiome in atopic dermatitis include a reduced bacterial diversity and increased abundance of Staphylococcus aureus. Topical antibiotics and antiseptics may decrease bacterial pathogens, but lack positive effects on microbiome diversity.

METHODS: In this double-blind, intraindividual vehicle-controlled pilot study, n = 20 patients received a gel containing a defined extract (Spiralin®) of the microalgae Spirulina platensis, previously shown to exert anti-microbial effects, or vehicle on target lesions of similar size and clinical activity. The Shannon index reflecting -diversity and the abundance of S. aureus were calculated from the analysis of 16s rRNA gene libraries with untreated non-lesional skin serving as control. Clinical activity was determined by the Target Lesion Severity Score (TLSS) and lesion size.

RESULTS: Positive effects of the active gel on the microbiome after 4 weeks of treatment were indicated by a significant increase of the Shannon index in areas treated with verum (mean increase 16.7%; p<0.01 vs. baseline), but not in areas treated with vehicle. This increase in verum-treated lesions was more pronounced in lesions with an at least 50% (26.3%) or an at least 75% reduction of the TLSS (33.3%). There was also a stronger decrease of the abundance of S. aureus in lesions treated with active gel compared to those treated with vehicle (25.5% vs. 9.4%), but significance was not met. There were several trends indicating clinical effects of the active gel. For example, vehicle-treated areas showed no reduction in area size (77.8 cm2 at week 4 compared to 77.0 cm2 at baseline), while verum-treated lesion area decreased on average by 6.9 cm2. Active and vehicle gel were well tolerated and very few local side effects were noted.

CONCLUSION: These preliminary results indicate a positive effect of a gel containing Spiralin® on the skin microbiome in patients with active atopic dermatitis (AD) lesions combined with reductions in clinical disease activity supporting further investigations of the active gel alone or in combination with anti-inflammatory treatments in larger AD studies.},
}

@article {pmid40913709,
year = {2025},
author = {Jamal, A and Kamal, MA and Alqurashi, YE and Al-Malki, ES and Naiyer, MM and Hussain, SA and Hattiwale, HM},
title = {The microbiome-cancer axis as a hidden contributor to early-onset tumorigenesis.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {10},
pages = {464},
pmid = {40913709},
issn = {1559-131X},
mesh = {Humans ; *Neoplasms/microbiology ; *Carcinogenesis/pathology ; *Gastrointestinal Microbiome ; *Microbiota ; Dysbiosis/microbiology ; Age of Onset ; },
abstract = {The global incidence of early-onset cancer has surged by nearly 80% over the past three decades, yet the underlying causes remain poorly understood. While genetics and lifestyle are among the traditional risk factors, emerging evidence implicates the human microbiome as a potent and overlooked contributor to early tumorigenesis. Increases in the studies that are exploring the tissue-specific microbiome signatures such as the enrichment of Actinomyces and Bacteroidia in early-onset colorectal cancer, or Enterobacter and Neisseria in pancreatic tumors offer compelling evidence for age-stratified microbial contributions. Additionally, the recent works on the establishment of gut-testis, oral-gut, and gut-liver microbial axes are being explored to understand the modulation of systemic immune and endocrine landscapes in younger individuals that might unravel their unique predisposition to malignancy. Further, the microbiome-cancer axis has been regarded as a hidden driver in the initiation and progression of early-onset malignancies across diverse tissue types. Understanding this link will provide the missing mechanistic insights showcasing how microbial dysbiosis, biofilm formation, and microbially derived metabolites promote oncogenic inflammation, DNA damage, and immune evasion contributing to early-onset cancers. Considering the potential of these studies, microbial biomarkers with diagnostic promises that include probiotics, fecal microbiota transplantation, and diet have also been explored as emerging tools for prevention and therapy. Through this study, we aim to understand early-onset cancer through a patient microbiota and underscore an urgent need to integrate microbial dynamics into cancer surveillance and intervention strategies, especially for young and largely asymptomatic populations.},
}

Humans
*Neoplasms/microbiology
*Carcinogenesis/pathology
*Gastrointestinal Microbiome
*Microbiota
Dysbiosis/microbiology
Age of Onset

@article {pmid40913635,
year = {2025},
author = {Ali, AQ and Mersal, EA and Samer, R and Alhjmohammad, SA and Alabdrabalridha, ZH and Alseeni, FY and Dawood, AF and Abdel All, MO and Abdelmoneim, AM and Shawky, TM},
title = {Berberine contributes to protecting against the cadmium-induced pancreatic damage: role of intestinal microbiome modulation and barrier function.},
journal = {Journal of molecular histology},
volume = {56},
number = {5},
pages = {296},
pmid = {40913635},
issn = {1567-2387},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Berberine/pharmacology ; *Cadmium/toxicity ; Rats ; Rats, Wistar ; Male ; *Pancreas/drug effects/pathology ; Intestinal Mucosa/drug effects/metabolism/microbiology ; *Protective Agents/pharmacology ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Cadmium (Cad) is a worldwide heavy metal pollutant associated with global health challenges. Alteration of the intestinal microbiome, due to chemicals' exposure, plays a vital role in the pathogenesis of gastrointestinal diseases such as pancreatic disorders. Hence, modulation of the gut microbiota might be a targeted approach to manage pancreatic diseases. Using murine modeling, this study consisted of two dependent experiments to investigate the curative potential of berberine (BBR) in a Wistar rat model of Cad-provoked pancreatic toxicity and the possible contribution of gut microbiota to BBR protection. In experiment 1, Cad-induced pancreatic injury was established in rats via 8-week oral gavage of Cad at 4 mg/kg. The treatment group was exposed to BBR at 200 mg/kg body weight, oral gavage for 8 weeks. In experiment 2, transplantation of the fecal microbiome was done, in which the fecal microbiota in each group of experiment 1 was orally gavaged to the healthy rats of each corresponding group in experiment 2, once weekly for 8 weeks. The serum amylase and lipase levels, pancreatic inflammatory and oxidative markers, histological, and immunohistochemical analyses were evaluated. The markers of gut mucosal barrier, and mRNA expression of cell junction proteins were investigated for possible intestinal injury. 16S rRNA sequencing was applied to identify the gut bacterial changes and possible pancreatic bacterial translocation. Cad induced intestinal barrier disruption and elicited a state of pancreatic inflammation and apoptosis as indicated by TGF-β and BAX immunohistochemistry, which were relieved by BBR. A decreased firmicutes/bacteroidetes ratio and microbial migration due to interrupted intestinal mucosal barrier were reported. Furthermore, BBR restored the bacterial richness and proportions in the gut, thereby maintaining the intestinal microbial community, fixing the intestinal mucosal barrier structure, and inhibiting the pathway of bacterial migration. BBR protected against Cad-induced pancreatic damage, mostly through safeguarding the intestinal barrier function. Modulation of the intestinal bacterial community, repairing the gut barrier structure, and interference with the pancreatic bacterial migration and colonization were suggested BBR effects, potentially alleviating Cad-related pancreatic injury.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Berberine/pharmacology
*Cadmium/toxicity
Rats
Rats, Wistar
Male
*Pancreas/drug effects/pathology
Intestinal Mucosa/drug effects/metabolism/microbiology
*Protective Agents/pharmacology
Disease Models, Animal
RNA, Ribosomal, 16S/genetics

@article {pmid40913400,
year = {2025},
author = {Zhong, H and Shi, Y and Kozlova, A and Moravcova, R and Rogalski, JC and Jamieson, A and Lansing, L and Moon, KM and Yuan, X and Gregoris, AS and Higo, H and Common, J and Conflitti, IM and Pepinelli, M and Tran, L and Cunningham, M and Jabbari, H and Bukhari, SA and French, SK and Polo, RO and Hoover, SE and Pernal, SF and Giovenazzo, P and Guarna, MM and Zayed, A and Foster, LJ},
title = {Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70033},
doi = {10.1002/pmic.70033},
pmid = {40913400},
issn = {1615-9861},
support = {AAFC J-002368//Government of Canada through Agriculture and Agri-Food Canada (AAFC) Genomics Research and Development Initiative (GRDI)/ ; AAFC J-002368//Government of Canada through Agriculture and Agri-Food Canada (AAFC) Genomics Research and Development Initiative (GRDI)/ ; AAFC J-002368//Government of Canada through Agriculture and Agri-Food Canada (AAFC) Genomics Research and Development Initiative (GRDI)/ ; LSARP #16420//Genome Canada/ ; LSARP #16420//Genome Canada/ ; OGI-185//Ontario Genomics Institute/ ; OGI-185//Ontario Genomics Institute/ ; 374PRO//Life Sciences Institute, and Genome BC/ ; 374PRO//Life Sciences Institute, and Genome BC/ ; },
abstract = {Honey bees (Apis mellifera) are vital pollinators in fruit-producing agroecosystems like highbush blueberry (HBB) and cranberry (CRA). However, their health is threatened by multiple interacting stressors, including pesticides, pathogens, and nutritional changes. We tested the hypothesis that distinct agricultural ecosystems-with different combinations of agrochemical exposure, pathogen loads, and floral resources-elicit ecosystem-specific, tissue-level molecular responses in honey bees. We conducted an integrated multi-omics analysis using RNA-sequencing (RNA-seq), proteomics, and gut microbiome profiling across three key tissue types (head, abdomen, and gut) of honey bees collected from two agroecosystems over two field seasons. Quantification was performed for pesticide residues, pathogen loads (Nosema spp., Varroa destructor, and multiple viruses), and gut microbiota. Weighted gene co-expression network analysis (WGCNA) revealed tissue-specific protein modules with ecosystem-associated patterns, which differed from RNA co-expression networks. Microbiome composition also varied, with key genera like Gilliamella, Snodgrassella, and Bartonella correlating with metabolic modules. These findings underscore the complex, environment-dependent impacts of agroecosystem conditions on bee health. Our study provides a system-level understanding of how combined pesticide, pathogen, and parasitic stressors, mediated by diet and microbiome, shape molecular phenotypes in honey bees-informing strategies for pollinator protection in managed landscapes. SUMMARY: This study provides a comprehensive multi-omics analysis of honey bees foraging in blueberry and cranberry agroecosystems, offering novel insights into the molecular mechanisms underlying pollinator health in managed crop environments. By integrating transcriptomic, proteomic, and microbiome profiling across key tissues-head, abdomen, and gut-we reveal how environmental stressors, including pesticide exposure, pathogen infections, and parasitic infestations (e.g., Varroa destructor), differentially impact bee physiology and microbiome composition. Our findings highlight tissue-specific responses to these stressors, with distinct metabolic pathway alterations observed in each tissue. Proteomic and transcriptomic analyses uncovered dysregulated pathways linked to oxidative phosphorylation and protein synthesis, while microbiome analysis revealed crop-dependent shifts in gut bacterial communities, suggesting potential roles in pesticide detoxification and immune modulation. Notably, we identified key molecular biomarkers associated with stress adaptation, which may serve as early indicators of colony health deterioration. This research underscores the need for a system-level approach to understanding pollinator stress in agricultural landscapes. By elucidating the interactions between diet, pesticide residues, pathogen loads, and molecular stress responses, our study provides a foundation for targeted conservation strategies aimed at mitigating environmental risks and improving pollination sustainability in agroecosystems.},
}

@article {pmid40913079,
year = {2025},
author = {Zhai, R and Zhang, H and Xie, Y and Zhang, S and Zhou, F and Du, X and Chen, W and Yan, Y and Zhang, J and Li, P and Atkinson, R and Wang, Z and Yang, C and Guan, Q and Ma, F and Xu, L},
title = {Naturally impaired side-chain shortening of aromatic 3-ketoacyl-CoAs reveals the biosynthetic pathway of plant acetophenones.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40913079},
issn = {2055-0278},
support = {CARS 28//Earmarked Fund for China Agriculture Research System/ ; 32102450//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Acetophenones, which show scattered distribution across phylogenetically distant plants and fungi, play diverse roles in plant-plant, plant-insect, plant-microbiome and even animal-insect interactions. However, the enzymatic basis of acetophenone biosynthesis in plants remains unknown. Here we elucidate the complete biosynthetic pathway of picein (4-hydroxyacetophenone glucoside) from 4-coumaroyl-CoA using pear (Pyrus) as a study system. We demonstrate that in certain pear cultivars, the acetophenone moiety originates from an impaired side-chain shortening reaction of an aromatic 3-ketoacyl-CoA intermediate, a key step in the β-oxidative biosynthesis of benzoic acid. This impairment results from a loss-of-function mutation in a peroxisomal 3-ketoacyl-CoA thiolase. The accumulated aromatic 3-ketoacyl-CoA is subsequently hydrolysed by a thioesterase and undergoes spontaneous decarboxylation to yield the acetophenone moiety. This rare metabolic phenomenon highlights that not only neofunctionalization but also loss-of-function mutations can drive diversification in plant secondary metabolism. Forward genetic approaches are powerful to shed light on such 'hidden' or recessive pathways in plants.},
}

@article {pmid40913049,
year = {2025},
author = {Park, H and Cheon, J and Kim, H and Kim, J and Kim, J and Shin, JY and Kim, H and Ryu, G and Chung, IY and Kim, JH and Kim, D and Zhang, Z and Wu, H and Beck, KR and Bäckhed, F and Kim, HJ and Lee, Y and Koh, A},
title = {Gut microbial production of imidazole propionate drives Parkinson's pathologies.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8216},
pmid = {40913049},
issn = {2041-1723},
support = {2023R1A2C1002876//National Research Foundation of Korea (NRF)/ ; RS-2024-00361688//National Research Foundation of Korea (NRF)/ ; RS-2024-00349023//National Research Foundation of Korea (NRF)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Parkinson Disease/microbiology/pathology/metabolism ; Mice ; *Imidazoles/metabolism ; Humans ; alpha-Synuclein/metabolism ; Male ; *Streptococcus mutans/metabolism/enzymology ; Dopaminergic Neurons/metabolism/pathology ; Female ; *Propionates/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Brain/metabolism/pathology ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Escherichia coli/genetics/metabolism ; Aged ; },
abstract = {Parkinson's disease (PD) is characterized by the selective degeneration of midbrain dopaminergic neurons and aggregation of α-synuclein. Emerging evidence implicates the gut microbiome in PD, with microbial metabolites proposed as potential pathological mediators. However, the specific microbes and metabolites involved, and whether gut-derived metabolites can reach the brain to directly induce neurodegeneration, remain unclear. Here we show that elevated levels of Streptococcus mutans (S. mutans) and its enzyme urocanate reductase (UrdA), which produces imidazole propionate (ImP), in the gut microbiome of patients with PD, along with increased plasma ImP. Colonization of mice with S. mutans harboring UrdA or Escherichia coli expressing UrdA from S. mutans increases systemic and brain ImP levels, inducing PD-like symptoms including dopaminergic neuronal loss, astrogliosis, microgliosis, and motor impairment. Additionally, S. mutans exacerbates α-synuclein pathology in a mouse model. ImP administration alone recapitulates key PD features, supporting the UrdA-ImP axis as a microbial driver of PD pathology. Mechanistically, mTORC1 activation is crucial for both S. mutans- and ImP-induced PD pathology. Together, these findings identify microbial ImP, produced via UrdA, as a direct pathological mediator of the gut-brain axis in PD.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Parkinson Disease/microbiology/pathology/metabolism
Mice
*Imidazoles/metabolism
Humans
alpha-Synuclein/metabolism
Male
*Streptococcus mutans/metabolism/enzymology
Dopaminergic Neurons/metabolism/pathology
Female
*Propionates/metabolism
Mice, Inbred C57BL
Disease Models, Animal
Brain/metabolism/pathology
Mechanistic Target of Rapamycin Complex 1/metabolism
Escherichia coli/genetics/metabolism
Aged

@article {pmid40912776,
year = {2025},
author = {Zhang, X and Lei, J and Qu, T and Zhang, X},
title = {Advances in chitosan-based materials for oral ulcer treatment.},
journal = {Carbohydrate polymers},
volume = {368},
number = {Pt 1},
pages = {124110},
doi = {10.1016/j.carbpol.2025.124110},
pmid = {40912776},
issn = {1879-1344},
mesh = {*Chitosan/chemistry/therapeutic use/pharmacology ; Humans ; *Oral Ulcer/drug therapy ; Hydrogels/chemistry ; Animals ; Nanoparticles/chemistry ; },
abstract = {Oral ulcers are a prevalent condition globally, causing significant pain and discomfort. The unique environment of the oral cavity, characterized by its humidity and dynamic nature, in conjunction with a diverse microbiome, presents challenges for traditional treatments for oral ulcers. Chitosan has emerged as a promising therapeutic agent for this condition. This review integrates findings from 34 peer-reviewed studies conducted between 2000 and 2025, with a focus on significant chitosan-based formulations. These formulations encompass hydrogel systems, microneedle systems, nanoparticle carriers, oral films, and nanofiber scaffolds. The evidence presented indicates that these chitosan-based materials display greater efficacy compared to conventional alternatives. Nevertheless, certain limitations remain, including transient adhesion, non-selective antimicrobial activity that may disrupt the commensal microbiota, and mechanical instability under the shear forces exerted by saliva. The integration of materials science and precision manufacturing holds the potential to yield next-generation chitosan platforms. In conclusion, this review elucidates the characteristics of oral ulcers, explores the biological activities of chitosan, and examines the diverse range of chitosan-based materials. The objective is to provide researchers and clinicians with valuable insights that can aid in the development and application of novel chitosan-based therapeutic strategies for managing oral ulcers.},
}

*Chitosan/chemistry/therapeutic use/pharmacology
Humans
*Oral Ulcer/drug therapy
Hydrogels/chemistry
Animals
Nanoparticles/chemistry

@article {pmid40912695,
year = {2025},
author = {Pauw, HS and Timmerhuis, HC and Besselink, M and Issa, Y and Bruno, M and de Jonge, PJF and van Goor, H and van Geenen, EM and Quispel, R and van de Vrie, W and Tan, A and Hadithi, M and Venneman, NG and Jansen, JM and Witteman, BJ and Schwartz, MP and van Wanrooij, RLJ and Voermans, RP and Poen, AC and van Duijvendijk, P and Anten, MPGF and Römkens, T and Sieswerda, E and Tielemans, MM and Hooft, JEV and Boermeester, MA and Verdonk, RC and van Santvoort, HC and van den Berg, FF},
title = {Identification of robust associations between admission microbiome profiles and complications of acute pancreatitis.},
journal = {BMJ open gastroenterology},
volume = {12},
number = {1},
pages = {},
doi = {10.1136/bmjgast-2025-001961},
pmid = {40912695},
issn = {2054-4774},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Middle Aged ; *Pancreatitis/complications/microbiology ; Saliva/microbiology ; Prospective Studies ; Adult ; Severity of Illness Index ; Rectum/microbiology ; Aged ; Netherlands/epidemiology ; RNA, Ribosomal, 16S/genetics ; Acute Disease ; Patient Admission/statistics & numerical data ; },
abstract = {OBJECTIVE: Patients with acute pancreatitis show reduced gut microbiome diversity and high abundance of pathogenic bacteria compared with healthy subjects. Admission microbiome profiles are increasingly linked to severity, but methodology and study quality hamper interpretation. Our aim was to investigate whether admission microbiome analysis provides robust and reproducible associations with severity and complications of acute pancreatitis.

METHODS: Patients with acute pancreatitis were prospectively enrolled from 20 Dutch hospitals (2019-2022). Admission saliva and rectal samples from 276 patients underwent 16S rDNA sequencing for microbiome profiling. Subgroups were defined based on a literature search. The microbiota endpoints (alpha- and beta-diversity, and genus abundance) were compared across subgroups and with previous studies. Robustness of the significant associations was classified as 'moderate' or 'high' in case of statistical significance in, respectively, 2 or ≥3 differential abundance models.

RESULTS: Rectal alpha diversity (Shannon Index 3.55 vs 3.63, p=0.026) was decreased in necrotising (n=49) versus oedematous pancreatitis (n=218). Microbiota communities of either saliva or rectal samples differed in all the subgroups. In total, 270 (rectal) and 138 (saliva) genera were associated with severity or complications, of which 35 and 3 (Anaeroglobus and Finegoldia in saliva; Lachnospiraceae_FE2018_group in rectal) were classified as, respectively, moderately and highly robust. Fourteen associations were previously reported, of which 10 were in the opposite direction compared with this study.

CONCLUSION: Three admission microbiome taxa associated with severity and complications were highly robust, although their biological relevance remains unclear. This study also shows the lack of replicable findings of admission microbiome associations, highlighting the need for longitudinal studies to establish temporal relationships between microbiome changes and disease progression.},
}

Humans
Male
*Gastrointestinal Microbiome/genetics
Female
Middle Aged
*Pancreatitis/complications/microbiology
Saliva/microbiology
Prospective Studies
Adult
Severity of Illness Index
Rectum/microbiology
Aged
Netherlands/epidemiology
RNA, Ribosomal, 16S/genetics
Acute Disease
Patient Admission/statistics & numerical data

@article {pmid40912674,
year = {2025},
author = {Branchi, BRR and Kiszewski, AE and Bonamigo, RR},
title = {Analysis of the main characteristics of children's skin moisturizers in the Brazilian market.},
journal = {Jornal de pediatria},
volume = {},
number = {},
pages = {101438},
doi = {10.1016/j.jped.2025.101438},
pmid = {40912674},
issn = {1678-4782},
abstract = {OBJECTIVE: One of the possible causes of skin microbiome imbalance is the use of dermocosmetics with inadequate pH. This study aims to critically evaluate several children's moisturizers regarding their characteristics so that we can verify the tendency of the products available on the market and whether they are slightly acidic. The importance of dermocosmetics formulated without ingredients with allergenic potential is also discussed in this work.

METHOD: Observational, analytical, cross-sectional and quantitative study. Several brands of children's moisturizers were selected and divided into two groups: group 1 (G1), with moisturizers focused on the care of children with normal skin; and group 2 (G2), with moisturizers with a therapeutic focus on atopic children. We analyzed the pH of each one of the moisturizers, as well as cost, presence of potentially allergenic components and other data contained in the packaging.

RESULTS: The members of G1 had an average pH of 5.81 ± 0.35, while the members of G2 had an average pH of 5.42 ± 0.28, with this difference being considered statistically significant (p ≤ 0.001). G1 differed in terms of cost, which was more affordable for the user, when compared to G2 (p ≤ 0.001), but with a predominance of potential allergens in its composition (p = 0.018).

CONCLUSION: This study demonstrates that all moisturizers analyzed in this study respected the acidic pH; however, the group of moisturizers with a therapeutic focus on atopic children had an even lower pH and lower allergenic potential in their composition compared to the group of moisturizers focused on care of children with normal skin.},
}

@article {pmid40912567,
year = {2025},
author = {Davaanyam, E and Otgonbaatar, U and Nakajima, A and Sakanaka, M and Ojima, MN and Kozakai, T and Katoh, T and Odamaki, T and Javzan, B and Dagvadorj, E and Bekh-Ochir, D and Katayama, T},
title = {Human milk oligosaccharides and infant gut microbiome in Mongolian mother-infant dyads.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26865},
pmid = {40912567},
issn = {1525-3198},
abstract = {Human milk oligosaccharides (HMO) play crucial roles in establishing a healthy gut microbiota in breastfed infants. Many studies have been conducted using samples collected in different areas with varying lifestyles to examine the relationships between milk HMO, infant gut microbiota, and microbial HMO consumption in feces. The present study analyzed the tripartite relationship using samples obtained from Mongolian mothers and infants living in herder and urban environments, a population underrepresented in previous research. Breast milk and infant feces were cross-sectionally collected from 74 mothers and 57 infants, respectively, with 57 samples obtained from mother-infant dyads. Permutational multivariate ANOVA (PERMANOVA) using maternal metadata revealed significant effects of secretor status and lactation period on milk HMO profiles, while lifestyle differences may have exerted a slight influence during early lactation. Comparison of the milk HMO profiles of Mongolian mothers with those of mothers from other countries revealed compositional similarities among Asian populations. Of the 37 Mongolian infants receiving mature milk, 36 infants had gut microbiotas rich in bifidobacteria with relative abundances ranging from 43% to 98%. In contrast, 20 neonates who received immature milk had microbiotas characteristic of an underdeveloped transitional stage. The PERMANOVA using infant metadata revealed an association of gut microbiota profiles with delivery mode among infants receiving mature milk. No association was detected with the mother's secretor status and lifestyle differences. Further analysis suggested that the bifidobacteria-dominant gut microbiota of Mongolian infants is established by HMO consumption and cross-feeding mediated by fucosyllactose transporters or Bifidobacterium bifidum.},
}

@article {pmid40912476,
year = {2025},
author = {Lu, Z and Petersen, C and Dai, R and Reyna, ME and Ahmadiankalati, M and Sifuentes, E and Dai, DLY and Hoskinson, C and Del Bel, KL and Miliku, K and Moraes, TJ and Mandhane, PJ and Becker, AB and Azad, MB and Simons, E and Lou, W and Ambalavanan, A and Duan, Q and Turvey, SE and Subbarao, P},
title = {Early preschool wheeze trajectories are predominantly non-allergic with distinct biologic and microbiome traits.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.07.034},
pmid = {40912476},
issn = {1097-6825},
abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective healthcare burden is critical for precise and effective interventions.

OBJECTIVE: We aimed to collectively define contributions and distinct characteristics of respiratory phenotypes based on longitudinal wheeze and atopic sensitization patterns in the first 5 years of life.

METHODS: Group-based trajectory analysis was performed in the CHILD Cohort study to identify distinct wheeze and allergic sensitization trajectories. Trajectories were evaluated for associated risk factors, healthcare utilization, biological determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles from infant microbiomes collected at 3-months and 1-year were assessed for phenotype-specific biomarkers.

RESULTS: Six distinct respiratory phenotypes were identified from 2902 children that differed by temporal wheeze and allergic sensitization patterns. While allergic wheeze phenotypes (11·6% of participants) carried the highest asthma diagnosis risk, the more common non-allergic phenotypes (88·3% of participants) contributed to the majority of 5-year asthma diagnoses (61·4% of diagnoses). Most importantly, non-allergic phenotypes accounted for over 2/3 of healthcare utilization in this age group. Phenotypes differed by lung function, blood eosinophils, allergic comorbidities and weight-for-age z-score. Moreover, microbiome profiles from 1439 infants revealed largely non-overlapping microbial signatures at 1 year were associated with each phenotype.

CONCLUSION: We identified novel early childhood respiratory phenotypes to disentangle non-overlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of non-atopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of healthcare utilization and asthma diagnoses.},
}

@article {pmid40912468,
year = {2025},
author = {Chen, H},
title = {Modifying microbial risk for colorectal neoplasia- a precision nutrition study of magnesium supplementation, TRPM7 genotypes, and gut microbiome.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.037},
pmid = {40912468},
issn = {1541-6100},
}

@article {pmid40912415,
year = {2025},
author = {Liu, X and He, J and Cui, L and Ye, Y and Luo, M and Xu, H and Zhai, Y and Zhao, Z and Huang, T and Li, Y and Wu, JL and Wen, J and Wang, Y and Zhou, T},
title = {Limosilactobacillus reuteri-Butyrate Axis in Depression Therapy: A Key Pathway Discovered Through a Novel Preclinical Human Flora-Associated Animal Model.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107941},
doi = {10.1016/j.phrs.2025.107941},
pmid = {40912415},
issn = {1096-1186},
abstract = {The transition from preclinical to clinical drug development is critically impeded by interspecies disparities, which limit the predictive validity of preclinical efficacy for human outcomes. To address this limitation, we established a human flora-associated depression rat (HFADR) model through fecal microbiota transplantation (FMT). The HFADR model bridges the preclinical-clinical translation by recapitulating conserved microbial-host interactions identified through multi-omics analysis in a chronic unpredictable mild stress (CUMS) rat model and in patients with major depressive disorder. The HFADR model simulated the pathophysiological characteristics of clinical depression validated by gut-brain axis indices, including microbial composition, inflammatory biomarkers, brain-derived neurotrophic factor (BDNF), and monoamine neurotransmitters. Employing geniposide, a bioactive iridoid compound derived from medicinal plants, as a therapeutic prototype, the HFADR model revealed the novel Limosilactobacillus reuteri-butyrate axis as a conserved regulatory hub for the treatment of depression. Geniposide administration restored L. reuteri abundance in the HFADR model, which significantly correlated with improved gut-brain axis homeostasis. Metabolomics confirmed that L. reuteri exerts antidepressant effects via butyrate restoration in CUMS mice, with parallel butyrate level alterations observed in geniposide-treated HFADR model. Both L. reuteri supplementation and exogenous butyrate administration reversed depression-like behavior, mechanistically confirming the axis by reduced hippocampal astrocyte activation and elevated Nrf2 expression. This study established the HFADR model as a translational tool for evaluating microbiota-targeted therapies and identified the L. reuteri-butyrate axis as a novel therapeutic target. Our findings provide a theoretical and practical framework for refining preclinical models and advancing antidepressant development using microbiome-based strategies.},
}

@article {pmid40912345,
year = {2025},
author = {Jin, Y and Alissa, M and Ahmed, AE and Al-Doaiss, AA and Asiri, N and Assiri, Y and Khan, SU and Khan, MU and Joseph, S},
title = {The Triadic Relationship Between Nonalcoholic fatty liver disease, Type 2 Diabetes, and cardiovascular disease: From Molecular Mechanisms to Clinical Management.},
journal = {Current problems in cardiology},
volume = {},
number = {},
pages = {103170},
doi = {10.1016/j.cpcardiol.2025.103170},
pmid = {40912345},
issn = {1535-6280},
abstract = {Nonalcoholic fatty liver disease (NAFLD) and type 2 diabetes mellitus (T2DM) represent interconnected metabolic disorders with multifaceted etiology, demonstrating bidirectional relationships and pronounced associations with cardiovascular diseases (CVDs). Despite extensive research, significant knowledge gaps persist regarding the temporal progression of these comorbidities, optimal screening strategies for high-risk populations, and personalized therapeutic approaches targeting the hepatic-cardiac-metabolic axis simultaneously. Current literature lacks a comprehensive analysis of phenotypic heterogeneity within NAFLD-T2DM-CVD clusters and fails to address sex-specific and ethnic variations in disease progression patterns adequately. A systematic literature search was conducted across PubMed, Medline, Embase, Web of Science, and Google Scholar databases from inception to June 2024, employing various combinations of terms including NAFLD, NASH, T2DM, and CVDs, with emphasis on identifying mechanistic pathways, epidemiological trends, and therapeutic innovations. This review identifies novel pathophysiological mechanisms linking hepatic steatosis, insulin resistance, and cardiovascular dysfunction, including previously underexplored roles of gut microbiome dysbiosis, advanced glycation end products, and epigenetic modifications. Emerging evidence suggests distinct molecular signatures that could facilitate precision medicine approaches. The intricate interplay between diabetes, hepatic dysfunction, and cardiovascular complications represents a global health challenge requiring integrated management strategies. Future research should prioritize developing biomarker-guided therapeutic algorithms, investigating sex-specific treatment responses, and establishing standardized protocols for concurrent NAFLD-T2DM-CVD management to optimize clinical outcomes and reduce healthcare burden.},
}

@article {pmid40912193,
year = {2025},
author = {Louca, P and Pericàs, JM and Lin, Y and Kouraki, A and Estévez-Vázquez, O and Martínez-Gómez, M and Cusidó, MS and Simpson, JP and Cubero, FJ and Homer, NZM and Valdes, AM and Menni, C},
title = {The gut-liver axis in progressive steatotic liver disease: A focus on bile acid dysregulation.},
journal = {The journal of nutrition, health & aging},
volume = {29},
number = {11},
pages = {100671},
doi = {10.1016/j.jnha.2025.100671},
pmid = {40912193},
issn = {1760-4788},
abstract = {INTRODUCTION: The gut-liver axis regulates metabolic homeostasis, with bile acids (BAs) serving as key signalling molecules. BA dysregulation is implicated in metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction- and alcohol-associated liver disease (MetALD), yet consistent identification of BA markers and their mechanistic roles across different stages of these diseases remain elusive.

METHODS: We integrated three complementary studies to examine BA dysregulation: a population-based cohort (1522 females from TwinsUK with serum BA and liver biomarker data), a clinical cohort (30 patients with steatotic liver disease, fibrosis stages F0-F4, and 4 controls), and rodent models (20 rats with MASLD/MetALD vs. 9 controls). BA profiles were quantified via LC-MS.

RESULTS: The primary bile acid taurocholate was consistently correlated with liver pathology: in TwinsUK, it associated with ALT (β [95%CI] 1.81 [1.27, 2.36], FDR < 0.05) both overall and when stratifying for age (<65 years, n = 923; ≥65 years, n = 599); in the clinical cohort, it was associated with F3 fibrosis (OR [95%CI] 8.56 × 10[-10] [3.80 × 10[-13], 1.93 × 10[-6]], FDR < 0.05); and in rodents, it was associated with MASLD/MetALD (OR [95%CI] 2.86 [1.17, 9.51], FDR < 0.05). The secondary bile acid taurochenodeoxycholate was associated with both early (F0, OR [95%CI] 13.63 [1.04, 179.17], p < 0.05) and advanced stages of disease (rodents, OR [95%CI] 15.41 [2.94, 311.82], FDR < 0.05).

CONCLUSION: Taurocholate and taurochenodeoxycholate emerge as consistent BA markers across liver disease stages, suggesting BA metabolism as potential therapeutic targets. This multi-model study bridges knowledge gaps in BA-driven mechanisms, informing personalised strategies for SLD management.},
}

@article {pmid40912182,
year = {2025},
author = {Wang, N and Shi, Y and Zhu, Y and Liu, Y and Zhang, Y and Wang, F and Zhang, Y and Kang, Z and Ding, X and Wei, Y and Li, J and Ding, GC},
title = {Long-term compost fertilization enhanced soil disease suppressiveness by fostering interactions between root exudates and the rhizosphere microbiome.},
journal = {Microbiological research},
volume = {302},
number = {},
pages = {128327},
doi = {10.1016/j.micres.2025.128327},
pmid = {40912182},
issn = {1618-0623},
abstract = {A comprehensive understanding of the interplay between agricultural practices and the rhizosphere microbiome particularly the role of root exudates is essential for harnessing microbial potential in sustainable agriculture. In this study, we investigated how disease-suppressive soil alters root exudate profiles in pepper plants and how these elevated exudates influence rhizosphere microbiome assembly and modulate the antagonistic activity of Bacillus methylotrophicus 400 (BM400) against Phytophthora capsici. GC-MS analysis identified distinct compositional profiles of root exudates in the disease-suppressive soil, with marked enrichment of seven compounds. Mini-rhizobox experiments revealed that a mixture of seven enriched compounds (MSEC) altered rhizosphere microbiome assembly, explaining 11 % of bacterial community variation, and selected for in vitro antagonists of P. capsici, particularly within 20 mm proximity to chemical injection sites. Chemotactic assays indicated that most enriched compounds attract and are metabolized by BM400, enhancing its motility. RNA-seq analysis further demonstrated that MSEC suppressed transcription of BM400 genes linked to protein synthesis and sporulation, while upregulating urease-encoding genes. Notably, MSEC-driven microbiome modulation exhibited regional specificity across soils from Shanghai, Guangdong, and Yancheng. In summary, disease-suppressive soil alters root exudate composition, promoting recruitment of beneficial microbial taxa potentially via chemotaxis, and sustains the activity of BM400 by suppressing genes associated with excessive metabolic activity and sporulation.},
}

@article {pmid40912150,
year = {2025},
author = {Zhang, Q and Yang, Y and Yang, Y and Shang, J and Su, S and Gao, P and Li, XX and Liu, Z and Kao, RY and Ko, BC and Thompson, B and Zhao, Q},
title = {A strategy to re-sensitise drug-resistant Gram-positive bacteria to oxazolidinone-class antibiotics.},
journal = {EBioMedicine},
volume = {119},
number = {},
pages = {105914},
doi = {10.1016/j.ebiom.2025.105914},
pmid = {40912150},
issn = {2352-3964},
abstract = {BACKGROUND: Multidrug-resistant bacterial infections have high mortality rates and few treatment options. Synergistic combinations may improve clinical outcome but traditional strategies often damage healthy microbiome. Oxazolidinone-class antibiotics are typical last-resort drugs for treating drug-resistant bacterial infections but are becoming less effective due to resistance development.

METHODS: After high-throughput screening, synergy was further assessed by in vitro indices (like fractional inhibitory concentration index, biofilm formation and resistance development) and in vivo symptoms in animals with skin and ocular bacterial infections (and ocular microbiome extraction analysis). Proteomics, chemical synthesis, multi-microscopy techniques and antibiotic real-time/kinetic accumulation were employed to explore mechanisms and expand translational applications.

FINDINGS: Combining phosphorylated oxazolidinone-class antibiotics with positively charged compounds (lysozyme as native representative) resulted in broad-spectrum drug re-sensitisation. In representative combination, urea cycle was disrupted to alkalinise cytoplasm, which subsequently activated alkaline phosphatase to promote conversion of phosphorylated prodrug to active form. By introducing concept of restored healthy microbiome as the evaluated index in antibiotic therapy, we confirmed excellent translational and microbiome-friendly potential of this strategy in clinical settings because it not only inhibited biofilm formation and development of drug-resistant mutations in vitro, but also alleviated symptoms in infected animals including the restoration of healthy microbiome.

INTERPRETATION: As both agents have excellent safety profiles, such clinical investigation may immediately be contemplated in humans. Translationally, scientists benefit from strategy by simultaneously achieving greater efficacy (>500-fold re-sensitisation) and higher safety (prodrug-based and microbiome-friendly strategy especially when active form may be toxic).

FUNDING: Collaborative Research Funds from Research Grants Council (C5033-19E).},
}

@article {pmid40912031,
year = {2025},
author = {Rouco, C and Triadó-Margarit, X and Abrantes, J and Lopes, AM and Almeida, T and Isla, J and de la Fuente, G and Rodriguez, O and Casamayor, EO},
title = {Changes in gut microbiota signatures associated with the epidemiological dynamics of wild European rabbits facing haemorrhagic disease outbreaks.},
journal = {Veterinary microbiology},
volume = {310},
number = {},
pages = {110688},
doi = {10.1016/j.vetmic.2025.110688},
pmid = {40912031},
issn = {1873-2542},
abstract = {The new variant of rabbit haemorrhagic disease virus (RHDV2 or RHDVb) is responsible for a lethal, emerging infectious disease in several species of lagomorphs, and is globally threatening wild rabbit populations. It is known that the gut microbiota plays a crucial role in modulating host health, including immune responses and disease susceptibility. We hypothesize potential association of gut microbiota with the epidemiological dynamics of RHDV2 outbreaks that may provide key insights into how this lethal, emerging pathogen impacts wild rabbit populations. We report on changes in the gut microbiota signatures associated with the epidemiological status of a wild population of European rabbits before, during, and after an RHD outbreak in NW Morocco. Two populations were also studied in NE Spain after an independent RHD outbreak. From each individual, we sampled liver, blood, and fresh hard faecal pellets to determine the presence of antigen (i.e. presence of RHDV RNA), antibodies against RHDV, and changes in gut microbiota composition after massive 16S rRNA gene analysis, respectively. Correlational analysis and differential abundance tests were carried out to unveil significant differences in the gut microbiota among the different serological and antigen profiles. A B/F ratio based on several selected taxa within the order Bacteroidales vs. several taxa within the phylum Firmicutes showed a threshold value of 1 that split susceptible (B/F <1) and non-susceptible individuals (B/F >1) both in Morocco and in Spain. The highest proportion of individuals B/F < 1 was found in juveniles, and 100 % of the juveniles RHD dead and 75 % of the adults RHD dead scored B/F < 1. Although the exact nature of this association remains to be determined, this work shows an interesting potential take-off to both explore RHDV2's ecological dynamics with regards to intestinal microbiota and developing potential targeted treatments or management strategies for conservation and pest control.},
}

@article {pmid40911549,
year = {2025},
author = {Paraiso, IL and Alcázar Magaña, A and Alexiev, A and Sharpton, TJ and Maier, CS and Kioussi, C and Stevens, JF},
title = {Reversing metabolic dysregulation in farnesoid X receptor knockout mice via gut microbiota modulation.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331040},
doi = {10.1371/journal.pone.0331040},
pmid = {40911549},
issn = {1932-6203},
mesh = {Animals ; *Receptors, Cytoplasmic and Nuclear/genetics/metabolism/deficiency ; *Gastrointestinal Microbiome/drug effects ; Mice, Knockout ; Diet, High-Fat/adverse effects ; Mice ; *Flavonoids/pharmacology ; Male ; *Propiophenones/pharmacology ; *Obesity/metabolism/microbiology/etiology/genetics/prevention & control ; Bile Acids and Salts/metabolism ; Mice, Inbred C57BL ; Lipid Metabolism/drug effects ; Liver/metabolism ; },
abstract = {The farnesoid X receptor (FXR), expressed in the liver and in the small intestine, is a key regulator of glucose and lipid metabolism. Its pharmacological modulation is explored as a potential treatment for obesity-related metabolic impairments. To develop effective pharmacological interventions, it is crucial to differentiate the individual contributions of intestinal and hepatic FXR to lipid metabolism. This study aimed to evaluate the impact of intestinal FXR ablation on gut microbiome composition and metabolic potential in high-fat diet (HFD)-fed mice. Additionally, we determined the genotype-specific effects of xanthohumol, a hop-derived ligand of FXR, known to mitigate metabolic dysfunction in HFD-fed mice. Intestinal FXR knockout prevented diet-induced obesity, a phenotype that correlated with a decrease in the predicted functional capacity of the gut microbiome. Intestinal FXR deficiency resulted in increased abundances of bacteria producing secondary bile acids, such as Oscillospira, and a decrease in beneficial bacteria, such as Akkermansia, both of which were mitigated by xanthohumol. Our findings provide insights to understand the contribution of intestinal FXR and gut microbiome to metabolic regulation under HFD conditions. We underscore the ability of xanthohumol to restore homeostasis, highlighting its potential to improve gut health.},
}

Animals
*Receptors, Cytoplasmic and Nuclear/genetics/metabolism/deficiency
*Gastrointestinal Microbiome/drug effects
Mice, Knockout
Diet, High-Fat/adverse effects
Mice
*Flavonoids/pharmacology
Male
*Propiophenones/pharmacology
*Obesity/metabolism/microbiology/etiology/genetics/prevention & control
Bile Acids and Salts/metabolism
Mice, Inbred C57BL
Lipid Metabolism/drug effects
Liver/metabolism

@article {pmid40911231,
year = {2025},
author = {Zhang, D and Long, M and Meng, L and Li, Y and Chen, B and Lin, D and Su, G},
title = {Molecular mechanisms of bone metastasis in breast cancer based on transcriptomic and microbiomic analysis.},
journal = {Cancer causes & control : CCC},
volume = {},
number = {},
pages = {},
pmid = {40911231},
issn = {1573-7225},
support = {SL2023A03J00259//Guangzhou Science and Technology Bureau/ ; },
abstract = {BACKGROUND: Bone metastasis (BM) in breast cancer affects patient prognosis, but its molecular mechanisms and relationship with the gut microbiome are not well understood. This study aims to explore gene expression and gut microbiome differences between BM and non-bone metastasis (BNM) patients, which could shed light on cancer progression and metastasis.

METHODS: We utilized a multi-omics approach, integrating transcriptomic and microbiomic data. Bioinformatics techniques including differential expression analysis, functional enrichment, protein-protein interaction network analysis, and LDA effect size analysis were applied. We also constructed miRNA regulatory networks and gene-gene interaction networks to identify key genes and microbial functions involved in BM.

RESULTS: The analysis identified significant upregulation of genes such as IBSP, PROM1, and IDO1 in BM patients. miRNA analysis suggested that let-7 family members might regulate these genes and influence cancer progression. Gene-gene network analysis revealed a synergistic role for genes like THBS1 and ITGB3 in tumor progression. Regarding the gut microbiome, BM patients exhibited enriched pathways related to arachidonic acid metabolism, steroid hormone synthesis, and thyroid hormone synthesis, potentially impacting immunity and metabolism. Additionally, Human papillomavirus (HPV) infection pathways were significantly enriched, indicating a possible role in BM.

CONCLUSION: The study highlights distinct gene expression and gut microbiome differences between BM and BNM patients. HPV infection may play a crucial role in BM development, offering new potential biomarkers and therapeutic targets for early diagnosis and treatment of BM in breast cancer.},
}

@article {pmid40911227,
year = {2025},
author = {Omar, TM and Alfarttoosi, KH and Sanghvi, G and Roopashree, R and Kashyap, A and Krithiga, T and Taher, WM and Alwan, M and Jawad, MJ and Al-Nuaimi, AMA},
title = {Engineering the Microbiome: a Novel Approach to Managing Autoimmune Diseases.},
journal = {Neuromolecular medicine},
volume = {27},
number = {1},
pages = {63},
pmid = {40911227},
issn = {1559-1174},
mesh = {Humans ; *Autoimmune Diseases/therapy/microbiology/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Inflammatory Bowel Diseases/therapy/microbiology ; Immune Tolerance ; Multiple Sclerosis/therapy/microbiology ; },
abstract = {Autoimmune diseases occur when the immune system mistakenly attacks the body's own tissues, affecting millions of people and often requiring long-term treatment. Current therapies, such as immunosuppressants and biologics, help manage symptoms but can cause serious side effects. A promising new approach involves engineered microbiota-a method that modifies gut bacteria to influence immune function and potentially ease autoimmune conditions. The gut microbiome is crucial in regulating immunity, and imbalances in its composition have been linked to diseases, such as rheumatoid arthritis (RA), multiple sclerosis (MS), and inflammatory bowel disease (IBD). Engineered microbiota works by altering microbial communities, either by adding new strains, genetically modifying existing bacteria, or using carefully selected groups of microbes to control inflammation and immune responses. Recent studies in both animal models and human trials suggest this approach could help restore immune tolerance, reduce inflammation, and repair the gut barrier. However, challenges remain, including ensuring safety, long-term effectiveness, and meeting regulatory standards. Despite being in its early stages, engineered microbiota holds great promise as a future treatment for autoimmune diseases, paving the way for more precise and personalized therapies that leverage the power of the microbiome to improve health.},
}

Humans
*Autoimmune Diseases/therapy/microbiology/immunology
*Gastrointestinal Microbiome/immunology/genetics
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Inflammatory Bowel Diseases/therapy/microbiology
Immune Tolerance
Multiple Sclerosis/therapy/microbiology

@article {pmid40911213,
year = {2025},
author = {Singh, V and Sun, J and Cheng, S and Kwan, AC and Velazquez, A},
title = {Obesity as a Chronic Disease: A Narrative Review of Evolving Definitions, Management Strategies, and Cardiometabolic Prioritization.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {40911213},
issn = {1865-8652},
support = {KL2TR001882/NH/NIH HHS/United States ; },
abstract = {Obesity is a multifactorial, complex disease that is driven by genetic, biological, environmental, and behavioral factors. In this review, we explain the key contributors to obesity, limitations in current definitions, its relationship with cardiometabolic health, and recent advancements in treatment. Obesity is characterized by the presence of excess and dysfunctional adipose tissue, driven by chronic inflammation and maladaptive energy homeostasis. Although body mass index (BMI) has historically been used to diagnose obesity, BMI provides a limited evaluation of individual patients because it fails to specifically quantify adiposity, which is the primary determinant of metabolic impact in these patients. There is an ongoing and necessary shift in treating obesity with a weight-inclusive approach that aims to address obesity upstream and prevent downstream cardiometabolic health complications. This approach is being supported by various treatment options, notably glucagon-like peptide-1 receptor agonists like semaglutide and tirzepatide, that also have promising effects on cardiovascular, renal, and liver health. Advances in precision medicine, gut microbiome research, and Multi-target therapies support personalized therapeutic approach. Despite these developments, less than 25% of individuals living with obesity are receiving evidence-based treatment. There is an urgent need to improve health care delivery to patients with obesity through timely, affordable, and multimodal treatments that promote sustainable and sustained weight loss. Increasing board certification of practicing physicians through the American Board of Obesity Medicine will be critical to improving access and quality of care.},
}

@article {pmid40911133,
year = {2025},
author = {Feng, C and Zhao, Y and He, Q and Yu, J and Sun, Z},
title = {Bifidobacterium breve B2798 and Its Heat-Killed Cells Alleviate Inflammation in Rats with DSS Model by Modulating Gut Microbiota.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40911133},
issn = {1867-1314},
support = {2022LJRC0003//Inner Mongolia Autonomous Region Science and Technology Leading Talent Team Project/ ; 2023YFF1104502//the National Key R&D Program of China/ ; 32325040//National Natural Science Foundation of China/ ; BR22-14-01//Basic Research Operating Expenses Program for Colleges and Universities directly under the Inner Mongolia Autonomous Region/ ; CARS36//the earmarked fund/ ; },
abstract = {While probiotics are widely recognized for their adjunctive benefits in ulcerative colitis treatment, the therapeutic potential of heat-killed cells remains underexplored. This study directly compared the efficacy of Bifidobacterium breve B2798 probiotics (LB group) and their heat-killed counterparts (DB group) in alleviating dextran sulfate sodium (DSS)-induced colitis in rats. Over a 21-day intervention, both treatments significantly mitigated colitis symptoms, including weight loss, colon damage, and splenomegaly, with heat-killed cells demonstrating superior histological improvement over live probiotics. Serum analysis revealed that both interventions normalized DSS-induced cytokine dysregulation, reducing pro-inflammatory markers and elevating anti-inflammatory. Although α-diversity remained stable, β-diversity analysis indicated distinct gut microbiota restructuring. Heat-killed cells uniquely enriched butyrate-producing Alistipes spp. and Parabacteroides distasonis, while probiotics upregulated Mucispirillum schaedleri and Odoribacter splanchnicus. Metabolomic profiling identified shared elevation of anti-inflammatory metabolites (linoleic acid, isorhamnetin) in both groups, yet heat-killed cells exhibited stronger modulation of metabolic pathways, including TCA cycle activation and pantothenate biosynthesis suppression. Correlation networks highlighted species-specific microbiota-metabolite-cytokine interactions, with Mucispirillum schaedleri and Barnesiella intestinihominis negatively associated with inflammatory markers (MPO, TNF-α). These findings demonstrate that while both live and heat-killed B. breve B2798 alleviate colitis, heat-killed cells exert enhanced regulatory effects on gut microbiota composition, metabolic pathways, and inflammatory responses, offering a safer alternative for inflammatory bowel disease management. Further mechanistic studies are warranted to validate these preclinical insights.},
}

@article {pmid40911023,
year = {2025},
author = {Zheng, M and Zhang, Y and Lin, X and Wang, H and Xu, M and Deng, X and Zheng, Z},
title = {Tissue-specific endophytic microbiome responses to "Candidatus Liberibacter asiaticus" in two citrus cultivars.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-07-25-1430-RE},
pmid = {40911023},
issn = {0191-2917},
abstract = {Citrus Huanglongbing (HLB), caused by "Candidatus Liberibacter asiaticus" (CLas), is a destructive disease threatening global citrus industry. Although citrus cultivars differ in HLB sensitivity, how infection alters endophytic bacterial communities in cultivars with contrasting susceptibility remains unclear. Here, we compared endophytic microbiome shifts in leaf and root tissue of HLB-susceptible Shatangju mandarin (C. reticulata cv. Shatangju) and HLB-tolerant Shatian pomelo (C. maxima cv. Shatian) at 10 months post grafting (MPG) with CLas-infected buds. Infected Shatangju mandarin showed severe symptoms and higher CLas levels in leaf than root, while infected Shatian pomelo remained asymptomatic with higher CLas in root than leaf. High-throughput 16S rRNA gene sequencing revealed that CLas infection restructured endophytic microbial community in tissue-specific manner. CLas-infected Shatian pomelo leaf displayed increased microbial diversity and network complexity, while CLas-infected Shatangju mandarin root harbored more disease-suppressive taxa like Streptomyces. Across both cultivars, network complexity correlated inversely with CLas abundance. Key genera (e.g., Pseudomonas, Streptomyces, Prevotella) correlated positively with CLas, suggesting roles in mitigating pathogen effects. Predicted functional profiling indicated activated pathways (amino acid metabolism, terpenoid/polyketide biosynthesis, xenobiotic biodegradation) potentially supporting host defense in infected tissues. The HLB tolerance of Shatian pomelo appeared linked to tissue-specific bacterial restructuring, particularly recruitment of antibiotic-producing bacteria and enhanced metabolic resilience. These findings elucidated cultivar-specific microbial strategies against CLas, offering insights for microbiome-mediated HLB management.},
}

@article {pmid40910796,
year = {2025},
author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R},
title = {The Earth Hologenome Initiative: Data Release 1.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf102},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação/ ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; },
abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.

RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.

CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}

Animals
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
Earth, Planet
*Vertebrates/genetics/microbiology
Databases, Genetic

@article {pmid40910778,
year = {2025},
author = {Aasmets, O and Taba, N and Krigul, KL and Andreson, R and , and Org, E},
title = {A hidden confounder for microbiome studies: medications used years before sample collection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054125},
doi = {10.1128/msystems.00541-25},
pmid = {40910778},
issn = {2379-5077},
abstract = {Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be "additive"-the more a medication is used, the stronger the impact on the microbiome. Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.IMPORTANCEThis is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.},
}

@article {pmid40910542,
year = {2025},
author = {Keely, S and Hoedt, EC and Pockney, P},
title = {Mechanical Bowel Preparation's Influence on the Microbiome in Anastomotic Leak.},
journal = {Diseases of the colon and rectum},
volume = {},
number = {},
pages = {},
doi = {10.1097/DCR.0000000000003956},
pmid = {40910542},
issn = {1530-0358},
}

@article {pmid40910526,
year = {2025},
author = {Xue, M and Lee, SH and Shao, J and Leibovitzh, H and Huynh, HQ and Griffiths, AM and Turner, D and Madsen, KL and Moayyedi, P and Steinhart, AH and Silverberg, MS and Deslandres, C and Bitton, A and Mack, DR and Jacobson, K and Ropeleski, MJ and Cino, M and Aumais, G and Bernstein, CN and Panaccione, R and Bressler, B and Espin-Garcia, O and Xu, W and Turpin, W and Croitoru, K and , },
title = {Metabolomics reveal distinct molecular pathways associated with future risk of Crohn's Disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2546998},
doi = {10.1080/19490976.2025.2546998},
pmid = {40910526},
issn = {1949-0984},
mesh = {Humans ; *Crohn Disease/microbiology/metabolism ; *Metabolomics ; Male ; Female ; Gastrointestinal Microbiome ; Adult ; Prospective Studies ; Biomarkers/blood ; Middle Aged ; Feces/chemistry/microbiology ; Metabolome ; Canada ; Bacteria/classification/genetics/metabolism/isolation & purification ; Case-Control Studies ; Risk Factors ; },
abstract = {Host - microbiome interactions are central to Crohn'sdisease (CD) pathogenesis; yet the early metabolic alterations that precededisease onset remain poorly defined. To explore preclinical metabolicsignatures of CD, we analyzed baseline serum metabolomic profiles in a nestedcase-control study within the Crohn's and Colitis Canada - Genetics, Environment, Microbiome (CCC-GEM) Project, a prospective cohort of 5,122 healthyfirst-degree relatives (FDRs) of CD patients. We included 78 individuals wholater developed CD and 311 matched FDRs who remained disease-free. In an untargetedassessment of metabolomic data, we identified 63 metabolites significantlyassociated with future CD risk. Integrative analyses further identifiedmultiple associations between CD-related metabolites and proteomic markers, gutmicrobiome composition, antimicrobial antibody, fecal calprotectin andC-reactive protein. Quinolinate, a tryptophan catabolite, was elevated inindividuals who later developed CD and showed strong positive correlations withC-reactive protein, fecal calprotectin, and C-X-C motif chemokine ligand 9 (CXCL9).In contrast, higher levels of ascorbate and isocitrate were associated withreduced CD risk and were negatively correlated with C-reactive protein and CD-associated proteins.These findings identify several distinct molecular pathways that contribute toCD pathogenesis.},
}

Humans
*Crohn Disease/microbiology/metabolism
*Metabolomics
Male
Female
Gastrointestinal Microbiome
Adult
Prospective Studies
Biomarkers/blood
Middle Aged
Feces/chemistry/microbiology
Metabolome
Canada
Bacteria/classification/genetics/metabolism/isolation & purification
Case-Control Studies
Risk Factors

@article {pmid40910443,
year = {2025},
author = {Huynh, LBP and Fan, HY and Huang, SY and Nam, NN and Nguyen, TT and Chen, YC},
title = {Influence of maternal dietary diversity during pregnancy on infant atopic dermatitis: Exploring the microbiome link in a Taiwanese birth cohort.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {9},
pages = {e70200},
doi = {10.1111/pai.70200},
pmid = {40910443},
issn = {1399-3038},
support = {NSTC 113 - 2628 - B - 038 - 006 - MY3//National Science and Technology Council, Taiwan obtained by Dr. Yang Ching Chen,/ ; },
mesh = {Humans ; Female ; *Dermatitis, Atopic/epidemiology/microbiology ; Pregnancy ; Taiwan/epidemiology ; Infant ; *Gastrointestinal Microbiome ; *Diet ; Infant, Newborn ; Birth Cohort ; Male ; Adult ; Longitudinal Studies ; *Prenatal Exposure Delayed Effects/epidemiology ; Incidence ; Child, Preschool ; *Maternal Nutritional Physiological Phenomena ; Cohort Studies ; },
abstract = {BACKGROUND: Maternal diet during pregnancy plays a critical role in shaping infant immune development, potentially influencing the risk of atopic dermatitis. However, the underlying mechanisms remain unclear. This study examined the association between maternal dietary diversity during pregnancy and the incidence of atopic dermatitis in early childhood and explored the potential mediating role of the infant gut microbiome.

METHODS: The Taipei Mother-Infant Nutrition Cohort study is a longitudinal birth cohort study tracking 677 mother-infant pairs from pregnancy to the children's third year. This study assessed maternal dietary diversity during pregnancy using the Food and Agriculture Organization's guidelines for Minimum Dietary Diversity for Women. Infant microbiota was analyzed at 2 months postpartum, and the incidence of atopic dermatitis in the offspring was monitored from birth to age three. Incidence risk was calculated using Cox proportional hazards regression with various confounders adjusted for. The study compared relative microbial abundances and alpha and beta diversity across different levels of maternal dietary diversity.

RESULTS: Higher maternal dietary diversity was associated with a lower risk of atopic dermatitis in offspring. Maternal dietary diversity did not significantly affect the alpha or beta diversity of the infant gut microbiome but influenced its composition. Greater abundance of Rothia and Parabacteroides genera was significantly associated with a lower risk of atopic dermatitis. Additionally, a higher relative abundance of the Parabacteroides genus was linked to maternal intake of Vitamin A-rich fruits and vegetables.

CONCLUSIONS: These findings suggest that greater maternal dietary diversity during pregnancy may be associated with a lower risk of atopic dermatitis in early childhood, potentially through modulation of the infant gut microbiome. Further studies are warranted to validate these associations and clarify underlying mechanisms.},
}

Humans
Female
*Dermatitis, Atopic/epidemiology/microbiology
Pregnancy
Taiwan/epidemiology
Infant
*Gastrointestinal Microbiome
*Diet
Infant, Newborn
Birth Cohort
Male
Adult
Longitudinal Studies
*Prenatal Exposure Delayed Effects/epidemiology
Incidence
Child, Preschool
*Maternal Nutritional Physiological Phenomena
Cohort Studies

@article {pmid40910376,
year = {2025},
author = {Malczewski, AB and Coward, JI and Ketheesan, N and Navarro, S},
title = {Immunometabolism: The role of gut-derived microbial metabolites in optimising immune response during checkpoint inhibitor therapy.},
journal = {Clinical and translational medicine},
volume = {15},
number = {9},
pages = {e70472},
pmid = {40910376},
issn = {2001-1326},
support = {CR0062020//Queensland Children's Hospital Foundation/ ; RCP10317//Queensland Children's Hospital Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy ; *Immunotherapy/methods ; },
abstract = {Checkpoint inhibitor therapy is the most common type of immunotherapy used in the clinical setting, however, there are significant obstacles with treatment resistance and cancer progression. Since its introduction, there have been relatively few advances in the development of prognostic or predictive biomarkers. The field of metabolomics studies small molecules and can provide us with an understanding of the dynamic events evolving during the tumour-drug-immune-system interaction. Several key pathways have emerged as important in understanding resistance mechanisms thereby providing a rationale for targeting immunometabolism in order to enhance the immune response during checkpoint inhibitor therapy. In the first part of this review, we explore the role of gut microbiome-derived short-chain fatty acids, which are recognized as important immunoregulatory molecules shaping T-cell activation, effector and memory function. We then discuss tryptophan catabolism as a key predictor of primary checkpoint inhibitor failure. Lastly, we focus on immunometabolism as an important future target in immunotherapy. ONE SENTENCE SUMMARY: This review focusses on microbiome-derived metabolites and their role in immunometabolism and the enhancement of checkpoint inhibitor responses.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Neoplasms/immunology/drug therapy
*Immunotherapy/methods

@article {pmid40910235,
year = {2025},
author = {Kaabi, YA},
title = {The Role of Gut Microbiota in Modulating Inflammation and Insulin Resistance in Type 2 Diabetes Mellitus: Implications for Complication Management.},
journal = {Current molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665240393897250826074023},
pmid = {40910235},
issn = {1875-5666},
abstract = {Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by insulin resistance and severe complications, including cardiovascular diseases, neuropathy, retinopathy, and nephropathy. This article examines the role of gut microbiota in modulating inflammation and insulin resistance in type 2 diabetes mellitus (T2DM), as well as its implications for managing complications associated with the disease. We analyzed published literature to elucidate mechanisms linking microbial dysbiosis, impaired gut barrier function, and chronic inflammation to glycemic control and T2DM complications. Key findings suggest that gut microbiota dysbiosis contributes to systemic inflammation and insulin resistance, thereby exacerbating the complications of type 2 diabetes mellitus (T2DM). Therapeutic strategies, such as probiotics, prebiotics, and fecal microbiota transplantation, promise to improve glycemic control and mitigate complications by restoring microbial balance. This review provides a comprehensive framework for understanding the role of the gut microbiota in type 2 diabetes mellitus (T2DM) and highlights potential therapeutic interventions to enhance the management of complications.},
}

@article {pmid40910202,
year = {2025},
author = {Pandey, AK and Mukherjee, S},
title = {Targeted Therapies and Computational Approaches in the Management of Crohn's Disease.},
journal = {Current gene therapy},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665232389255250818093932},
pmid = {40910202},
issn = {1875-5631},
abstract = {Crohn's disease (CD), a chronic inflammatory disorder of the gastrointestinal tract, presents significant challenges in clinical medicine due to its multifactorial etiology and varied therapeutic responses. This review examines the diverse causes of CD, including genetic predispositions identified through genome-wide association studies (GWAS), which involve scanning the genome for single-nucleotide polymorphisms associated with CD risk, as well as environmental triggers, such as diet and alterations in the microbiome. Biomarkers, such as fecal calprotectin and Creactive protein (CRP), as well as genetic markers like NOD2 mutations, provide critical tools for diagnosis and treatment stratification. Advances in computational methodologies, including multiomics analyses and machine learning, have enhanced our understanding of CD pathophysiology and therapeutic outcomes. Traditional treatments, including immunomodulators and biologics, such as anti-TNF agents, have laid the groundwork for novel cytokine-targeted therapies, such as IL-12/23 inhibitors (e.g., ustekinumab) and integrin inhibitors (e.g., vedolizumab), which aim to improve mucosal healing and reduce relapse rates. However, integrating personalized medicine into clinical practice remains challenging due to the heterogeneity of CD and limitations in biomarker validation. The integration of predictive biomarkers with computational tools enables clinicians to tailor therapy at the individual level, improving remission rates, minimizing adverse effects, and enhancing long-term disease control. These personalized strategies show promise in shifting CD management toward a more effective, patient-specific model of care. This review underscores the potential of personalized therapeutic strategies, leveraging molecular and computational insights, to optimize disease management and improve patient outcomes in CD.},
}

@article {pmid40909933,
year = {2025},
author = {Florkiewicz, AB and Fijałkowski, P and Fijałkowski, P and Złoch, M and Ludwiczak, A and Gabryś, D and Miśta, W and Mrochem-Kwarciak, J and Jędrzejewska, A and Telka, E and Rabsztyn, M and Czeszewska-Rosiak, G and Mametov, R and Tretyn, A and Pomastowski, P},
title = {Bacteriological Identification, Characterization and Changes of Feces Microbiome in Prostate Cancer Patients Undergoing Radiotherapy.},
journal = {Cancer management and research},
volume = {17},
number = {},
pages = {1825-1841},
pmid = {40909933},
issn = {1179-1322},
abstract = {PURPOSE: To investigate the bacteriological characteristics of the gut microbiome in patients with prostate cancer and changes during and after radiation therapy.

PATIENTS AND METHODS: Forty-one prostate cancer (PCa) patients treated with radiation therapy were included in the study. Fecal samples were collected at three points: before gold marker implantation into the prostate gland (K1), at the start (K2), and last day of radiotherapy (K3). Microbial identification was performed using MALDI-TOF MS, which allowed for precise identification at the species and genus levels. Blood biochemical parameters were assessed, and correlation analyses were performed.

RESULTS: In total, 291 microbial isolates were identified, with the most common genera being Escherichia (N=120), Streptococcus (N=31), and Enterococcus (N=30). A significant decrease in E. coli was observed in K3 compared with K1 and K2, whereas Citrobacter appeared exclusively at K2. Additionally, liver enzyme levels decreased, and IL-6 levels increased during treatment. These findings indicate significant shifts in the gut microbiota due to radiotherapy.

CONCLUSION: Radiation therapy alters the gut microbiota composition in patients with PCa, reduces microbial diversity, and promotes the growth of opportunistic pathogens. These changes are linked to biochemical parameters, suggesting a potential impact on health. Further research is needed to explore microbiome-targeted interventions during treatment.},
}

@article {pmid40909931,
year = {2025},
author = {Al Noman, A and Alhudhaibi, AM and Afroza, M and Tonni, SD and Shehab, HM and Jahan Iba, N and Taha, TH and Abdallah, EM},
title = {Neuroplasticity and the microbiome: how microorganisms influence brain change.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629349},
pmid = {40909931},
issn = {1664-302X},
abstract = {Neuroplasticity, the brain's ability to reorganize and adapt, has traditionally been attributed to external stimuli, learning, and experience. However, emerging research highlights the gut microbiota as a key modulator of neuroplasticity through the gut-brain axis. This review examines the mechanisms by which intestinal microorganisms influence brain function, including microbial metabolite production, immune system modulation, neurotransmitter synthesis, and hormonal regulation. Dysbiosis, or microbial imbalance, has been linked to neurodevelopmental disorders, major depressive disorder (MDD), and cognitive impairments, emphasizing the microbiome's role in psychiatric and neurological health. Animal and human studies suggest that microbiota-targeted interventions, such as probiotics, prebiotics, and dietary modifications, may enhance neuroplasticity and mitigate mental health disorders. Future research should focus on understanding direct microbial-neuronal interactions and developing personalized microbiome-based therapies. This study underscores the gut microbiota's potential as a novel target for improving brain plasticity and mental health outcomes.},
}

@article {pmid40909930,
year = {2025},
author = {Ha, AD and Howe, DK and Colton, AJ and Mc Donnell, RJ and Denver, DR},
title = {Microbiome dynamics associated with the infection of grey field slugs by the biocontrol nematode Phasmarhabditis hermaphrodita.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1619231},
pmid = {40909930},
issn = {1664-302X},
abstract = {The facultative-parasitic nematode Phasmarhabditis hermaphrodita has been used for many years as a biological control agent targeting slug pests. During the nematode's infection process, the presence of certain bacteria has been suggested to affect the pathogenicity and efficiency of the nematodes in killing slugs, though the potential roles of different bacteria in affecting host-infection by nematodes remain unclear. In this study, we examined three experimental P. hermaphrodita populations cultured with three different bacteria: 1) Escherichia coli (EC), 2) a newly isolated Pseudomonas sp. strain (PS) that co-cultured with a P. hermaphrodita strain found in Oregon, USA, and 3) the original complex bacterial community (BC) associated with the nematode. For each treatment, we evaluated the pathogenicity of P. hermaphrodita at low and high concentrations towards adult grey field slug Deroceras reticulatum and investigated changes in the nematode microbiome structure before and after slug infection. Slugs exposed to EC, of both low and high concentration treatments, survived significantly longer than slugs exposed to PS high and BC high. Slugs in the BC low treatment survived significantly longer compared to BC high, but significantly shorter compared to EC high. We identified a wide variety of taxa components (82 genera) in the community associated with the nematode pre-infection, most of which were of low abundance. In all bacterial treatments post-infection, the number of genera almost quadrupled and the abundance of these taxa changed remarkably, although the taxa with the highest abundance remained stable. We also observed four Pseudomonas amplicon sequence variants (ASVs) that increased in abundance after slug infection in the Pseudomonas treatment. This finding suggests these taxa may play a role in the infection process, potentially acting as opportunistic pathogens, or facilitating infection progression through providing nematodes with a favorable food source, or contributing directly to the nematode's virulence.},
}

@article {pmid40909921,
year = {2025},
author = {Shi, M and Wang, LF and Hu, WT and Liang, ZG},
title = {The gut microbiome in lung cancer: from pathogenesis to precision therapy.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1606684},
pmid = {40909921},
issn = {1664-302X},
abstract = {The gut microbiome has emerged as a key modulator of immune responses and treatment efficacy in oncology. Growing evidence links gut dysbiosis to resistance against immune checkpoint inhibitors (ICIs) in advanced cancers, prompting exploration of the gut-lung axis-a bidirectional network connecting intestinal microbiota with pulmonary health. Given lung cancer's status as the leading cause of cancer mortality worldwide, understanding this axis holds significant therapeutic potential. This review synthesizes current knowledge on gut microbiota's role in lung cancer development, diagnosis, and treatment. We highlight microbial signatures predictive of disease and therapy response, discuss microbiota-targeted interventions (e.g., probiotics, Fecal Microbiota Transplantation), and elucidate mechanistic insights into microbial-immune crosstalk. Finally, we outline future directions for leveraging the gut microbiome in personalized lung cancer management.},
}

@article {pmid40909897,
year = {2025},
author = {Li, J and Zhang, H and Wang, T and Peng, L and Huang, K and Tang, X and Li, W and Xu, Z and Li, C and Chen, F and Qiu, H and Xu, J and Cheng, Y},
title = {Functional differentiation of industrial hemp rhizosphere microbiome along environmental gradients.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1578662},
pmid = {40909897},
issn = {1664-462X},
abstract = {The southwestern, central, and northeastern regions of China are the primary cultivation areas for industrial hemp. Microorganisms within the soil-root continuum play a crucial role in plant health. However, the mechanisms by which these microbial communities respond to environmental gradients remain unclear. This study aimed to explore how bacterial and fungal communities in the bulk soil and rhizosphere of industrial hemp respond to environmental gradients across diverse climatic zones. We collected soil samples from eight representative regions and analyzed microbial diversity, composition, and assembly mechanisms using DNA metabarcoding. Results showed that microbial diversity in the rhizosphere was lower than in bulk soil, likely due to selective root filtering. The lowest diversity occurred in the temperate continental climate, highlighting the effects of precipitation, soil nutrients, and organic carbon. Climate type was the main factor influencing microbial community structure, with annual precipitation and temperature as key environmental constraints. Bacterial communities were mainly assembled by deterministic processes, while fungal communities were driven by stochastic processes. Additionally, geographic variation in rhizosphere microbial function reflected a co-adaptive mechanism between hemp and its microbial community under varying environmental pressures. These findings enhance our understanding of industrial hemp soil microbiomes and provide insights for optimizing cultivation management.},
}

@article {pmid40909844,
year = {2025},
author = {Hussain, FA and Bergerat, A and Kelly, J and Demidkina, BC and Worrall, D and Xu, J and Kannan, A and Brunner, T and Culler, N and Goldenberg, M and Arar, WE and Katukota, AV and Murthy, M and Elsherbini, J and Hussain, S and Dong, M and Kwon, DS and Mitchell, CM},
title = {Donation strain engraftment demonstrates feasibility of vaginal microbiota transplantation to prevent recurrent bacterial vaginosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.27.25334544},
pmid = {40909844},
abstract = {Although bacterial vaginosis (BV) affects 30% of women worldwide and is associated with adverse health outcomes, current standard-of-care antibiotics fail in over half of cases and treatments have not improved in over 40 years. Probiotics have been proposed as alternative treatments, but fail to restore an optimal lactobacilli-dominated microbiome in the vast majority of patients. Here, we present findings from a pilot clinical trial demonstrating the successful engraftment of vaginal microbiota transplantations (VMTs) after antibiotic treatment in individuals with recurrent BV. Following an investigational donation protocol under an FDA IND, we treated eight recipients with material from a single donor. Using 16S rRNA gene amplicon sequencing we show that VMT results in a shift toward an optimal, Lactobacillus crispatus -dominated microbial community in three out of four VMT recipients at one month post-transplant. In two successful transplantations, this shift lasted at least six months post-VMT. In contrast, no placebo recipients exhibited L. crispatus dominance. Bacterial culturing and whole genome sequencing combined with metagenomic sequencing from donations and recipient longitudinal samples revealed colonization by donor-derived strains of L. crispatus in VMT recipients. Additionally, we observed no increase in genital inflammatory markers or changes in endocervical immune cell proportions when comparing treatment to placebo, indicating transplant safety. Together, these findings support the hypothesis that transferring the entire vaginal microbiota can lead to a more complete restoration of the vaginal ecosystem compared to single strain probiotics and lay the foundation for designing novel microbial therapies for BV. Vaginal microbiota transplantations lead to stable L. crispatus engraftment in the microbiomes of certain patients with recurrent bacterial vaginosis.},
}

@article {pmid40909795,
year = {2025},
author = {Cheatham, S and Rehman, Z and Arastonejad, M and Kane, R and Ahmad, N and Luffman, N and Harada, H and Zhang, Y and Tyc, K and Gewirtz, D and Akbarali, HI},
title = {Butyrate Modulates Intestinal Microbiome and Epithelial Function to Attenuate Irinotecan-induced GI Toxicity.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7436690/v1},
pmid = {40909795},
issn = {2693-5015},
abstract = {Chemotherapy-induced gastrointestinal toxicity is a significant dose-limiting complication for cancer treatment. Disruption of the gastrointestinal (GI) epithelial barrier function by several chemotherapeutic agents results in development of mucositis and diarrhea. Thus, maintaining barrier integrity may be of therapeutic benefit. Recent studies have shown the beneficial effects of the microbial metabolite butyrate, a short chain fatty acid (SCFA), on epithelial barrier integrity. In this current study, we tested the effect of oral butyrate on irinotecan-induced gastrointestinal (GI) toxicity in mice. Irinotecan dose-dependently reduced body weight and increased fecal water content. Nicotine-induced inward currents in ileum myenteric neurons were significantly increased in irinotecan treated mice consistent with enhanced GI motility. Loperamide reduced GI motility of irinotecan treated mice, however tolerance developed with chronic use, consistent with clinical findings of loperamide refractory diarrhea in patients. Oral butyrate improved epithelial permeability, prevented loss in stem cell marker, lgr5 in colonic crypts and muc2 expression in ileum. Butyrate also prevented irinotecan-induced increase in β-glucuronidase activity in fecal samples. Irinotecan treatment produced a significant shift in the β diversity of the fecal microbiome that was mitigated by butyrate. The microbial dysbiosis was associated with increases in the mucin degrading bacteria Akkermansia muciniphilia and the hydrogen sulfide producing Desulfovibrio sp10575755 that was reduced with butyrate treatment.},
}

@article {pmid40909779,
year = {2025},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-Level microbial signatures and inferred functional alterations in infants with Food Protein-Induced Allergic Proctocolitis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7112201/v1},
pmid = {40909779},
issn = {2693-5015},
abstract = {The complex relationship between the gut microbiome and immune system development during infancy is thought to be a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.Here we show that infants with AP exhibit microbial compositions that differ from unaffected controls, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while protective species like Bifidobacterium breve and Klebsiella species are more abundant in unaffected controls. Strain-level analyses uncovered additional disease-linked patterns, particularly Lacticaseibacillus rhamnosus strains showed strong association with probiotic use and predominantly found in infants with AP. These findings reveal disease-associated microbial signatures that can sometimes be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-specific lineages with distinct gene content profiles that were not previously recognized. Genes for biofilm formation and cell adhesion in E. coli , for example, were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and establish a foundation for future efforts to identify early microbial biomarkers and potential interventional targets for AP. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.},
}

@article {pmid40909656,
year = {2025},
author = {Lyon, PD and Leesang, TE and Brabson, JP and Do, K and Dalzell, M and Nivelo, LA and Lam, MQ and Peci, A and Fang, B and Strippoli, V and Armand, AA and Singh, PK and Roy, S and Beckedorff, F and Villarino, AV and Cimmino, L},
title = {B12 promotes gut dysbiosis and an inflammatory microenvironment that potentiates Tet2 -deficient hematopoiesis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.22.671600},
pmid = {40909656},
issn = {2692-8205},
abstract = {Recent studies have linked elevated vitamin B12 serum levels with the presence of clonal hematopoiesis (CH) and an increased risk of developing myeloid malignancy. High B12 supplementation increases serum levels, alters gut microbial composition, and reduces the production of short-chain fatty acids (SCFAs), which help maintain gut barrier function and mucosal integrity. TET2 mutation is a frequent driver of CH that progresses in a positive feedback loop in response to microbial signals suggesting that B12 may influence CH via the gut microbiome. We evaluated the microenvironmental effects of B12 supplementation in a Tet2 -deficient model of CH and found that B12 enhances myelopoiesis, heightens the responses of myeloid cells to bacterial stimuli, and increases the levels of circulating inflammatory cytokines. B12 supplementation also induced gut dysbiosis and reduced the levels of SCFA-producing bacteria in both wild-type and Tet2 -deficient mice. Importantly, the effects of excess B12 were reversible upon oral supplementation with the SCFA butyrate. These findings suggest that B12 may promote CH progression by disrupting microbiome-derived SCFA metabolism, highlighting a potential therapeutic role for SCFA supplementation in mitigating CH.},
}

@article {pmid40909525,
year = {2025},
author = {Jena, S and Lawore, D and Briones, JM and Birse, K and Lamont, A and Mackelprang, RD and Noel-Romas, L and Perner, M and Hou, X and Irungu, E and Mugo, N and Knodel, S and Brubaker, SD and Muwonge, TR and Katabira, E and Hughes, SM and Calienes, FL and Krajci, R and Liu, R and Nemecio, D and Celum, C and Hladik, F and Lingappa, J and Burgener, AD and Berard, AR and Green, LN and Brubaker, DK},
title = {Identifying a Vaginal Microbiome-Derived Selective Antibiotic Metabolite via Microbiome Pharmacology Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.28.672927},
pmid = {40909525},
issn = {2692-8205},
abstract = {The vaginal microbiome plays a critical role in maintaining immune and epithelial homeostasis in the female reproductive tract. Bacterial Vaginosis (BV) is deleterious to female health, causing the loss of beneficial Lactobacillus species, overgrowth of anaerobic taxa, changes in vaginal pH, breakdown of protective mucins and epithelial barriers, and activation of the immune system. Treatment with gel-based antibiotics (Metronidazole or Clindamycin) resolves BV for 85% of patients, but 50% of those cases recur, indicating a need to identify strategies for overcoming antibiotic resistance and achieving a more durable response. Here, we developed a systems biology approach termed Microbiome Pharmacology Analysis to characterize the antibiotic potential of vaginal microbes, their metabolites and functions, via computational fusion of human cohort multi-omics and post-drug perturbation transcriptomic profiles. We focused on Clindamycin and Metronidazole as candidate drugs and screened 780 vaginal microbiome-drug mimicry candidates to identify candidate taxa and metabolites with antibiotic potential. We demonstrate experimentally that Lactobacillus crispatus -derived Hydroxyisocaproate (HICA) selectively kills Gardnerella vaginalis and that HICA enhances epithelial barrier integrity in a human vagina-on-a-chip system. Our work demonstrates the first use of Pharmacobiome Analysis , for discovering novel, selective antibiotic metabolites for BV with implications for charting the full pharmacologic potential of the vaginal microbiome.},
}

@article {pmid40909511,
year = {2025},
author = {Caro, TA and Kashyap, S and Maloney, AE and Hoyt, DW and Kubo, MD and Hoehler, TM and Templeton, A},
title = {Dissolved inorganic carbon supports robust anabolism and methanogenesis in actively serpentinizing rocks.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.25.672207},
pmid = {40909511},
issn = {2692-8205},
abstract = {Serpentinites, hydrated ultramafic rocks that produce [hyper]alkaline, reducing, H2-rich groundwaters, host subsurface microbial ecosystems. Though in the presence of enormous reducing power, life in serpentinizing systems is limited by oxidant and carbon availability. The forms of carbon that support the serpentinite-hosted microbiome, and their rates of biological assimilation, remain poorly understood. In this work, we quantify the habitability of subsurface environments shaped by serpentinization and examine the forms of carbon that support their microbial constituents, focusing specifically on dissolved inorganic carbon, acetate, and formate. We access reacted groundwater from the largest terrestrial serpentinizing body and measure carbon assimilation at the single-cell level. Across all conditions, we consistently observe robust assimilation of dissolved inorganic carbon into microbial biomass. Notably, we find that dissolved inorganic carbon supports the majority of methanogenic activity in the system, even at hyperalkaline conditions (pH > 11). Inferred bioenergetic fluxes suggest that rates of biological hydrogen-consumption and methanogenesis are relevant at the landscape scale. We identify a strong potential for the microbiome to be stimulated by increases in H2 and CO2, a finding with implications for the search for life on other planetary bodies and for the growing deployment of fluid injection technologies in ultramafic rocks, such as geological hydrogen production or carbon mineralization.},
}

@article {pmid40909440,
year = {2025},
author = {Feng, M and Chai, Y and Li, J and Wang, Q and Zhang, D},
title = {A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1619911},
pmid = {40909440},
issn = {1664-8021},
abstract = {BACKGROUND AND PURPOSE: In recent years, research on the relationship between hepatitis B virus-related cirrhosis (HBV-LC) and gut microbiota has grown, but studies focusing on the Northwest Chinese population are scarce. This study characterized the gut microbiota composition and function in HBV-LC patients vs. healthy individuals in Northwest China, aiming to provide a scientific basis for region-specific precision therapies.

MATERIALS AND METHODS: A cross-sectional study enrolled 43 HBV-LC patients and 43 age-/sex-matched healthy controls (HC) from Gansu Province. Clinical parameters including liver function, blood routine, coagulation function, blood biochemistry were measured. Shotgun metagenomic sequencing was conducted to analyze gut microbiota taxonomic composition and function.

RESULTS: HBV-LC patients showed significantly elevated alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), γ-glutamyl transferase (γ-GGT), prothrombin time, international normalized ratio (INR), and thrombin time, but reduced triglycerides (TG), total cholesterol (TC), erythrocytes, thrombocytes, total protein, albumin, and prothrombin time activity (PT-ratio). Alpha-diversity based on Shannon and Simpson indices was lower in HBV-LC. At the genus level, Bacteroides, Prevotella, Escherichia, Parabacteroides, Veillonella, and Klebsiella were enriched in HBV-LC, while Bifidobacterium, Faecalibacterium, Roseburia, Ruminococcus, Anaerostipes, Blautia, Eubacterium, and Fusicatenibacter were reduced. Species-level analysis identified distinct enrichment of Prevotella copri, Bacteroides vulgatus, Escherichia coli, Fusobacterium nucleatum, and Veillonella spp. in HBV-LC. Functional analysis revealed 482 metabolic pathways. HBV-LC showed enhanced lipid, amino acid, and nucleotide metabolism, menaquinol biosynthesis, and anaerobic energy metabolism, but reduced acetate/lactate production, lactose/galactose degradation, and peptidoglycan biosynthesis. Metagenome-wide association study revealed HBV-LC-enriched opportunistic species (e.g., E. coli, Veillonella spp.) correlated positively with hepatic enzymes and coagulation parameters, and negatively with TC, TG, and erythrocyte counts.

CONCLUSION: HBV-LC patients in Northwest China exhibit altered clinical indicators, gut microbial composition (reduced diversity, increased opportunistic pathogens, decreased beneficial species), and metabolic function. These findings highlight the potential of gut microbiome-targeted interventions for regional precision medicine of HBV-LC.},
}

@article {pmid40909341,
year = {2025},
author = {Shaw, CA and Verstrate, M and Graniczkowska, K and Risoen, KR and Dini, P and Weimer, BC},
title = {The use of stem cells and organoids for modeling host-microbe interactions in low-biomass tissues.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1641366},
pmid = {40909341},
issn = {2235-2988},
mesh = {*Organoids/microbiology ; Humans ; *Stem Cells/microbiology ; *Host Microbial Interactions ; Animals ; *Host-Pathogen Interactions ; Microbiota ; Models, Biological ; Regenerative Medicine/methods ; },
abstract = {Stem cells and organoids have emerged as pivotal biological tools for biologically relevant models. Together, these in vitro models realistically recapitulate structural and functional elements of the in vivo organ, allowing for studies of cellular, molecular, and genetic features that underpin various diseases that are difficult to observe in low-biomass tissues. Stem cells, and more recently organoids, have been applied in vivo as regenerative therapies. The emergence of the microbiome as an occupant throughout different body locales requires new approaches to understand the complex cellular interactions with the host tissue at each site. The success of regenerative medicine strategies and therapeutic development is intricately linked to this understanding and management of host-microbe dynamics. Interactions with the host microbiome and infections can both significantly impair tissue regeneration and compromise the function of stem cell-derived therapies. Therefore, a comprehensive understanding of how pathogens and the microbiome interact with stem cells and organoids is relevant for developing safe and effective regenerative medicine interventions. This review explores the evolving landscape of organoid technology, including a discussion on the importance of stem cell studies and considerations for organoid development that are important for use as models to study microbiome interactions. Additionally, this work describes the pivotal role of cell culture models in advancing host-microbe interaction studies in understudied low-biomass organs such as the stomach and reproductive tract. Through this assessment, we aim to shed light on the potential of these models to transform the approach to studying and managing infectious diseases within the context of regenerative medicine.},
}

*Organoids/microbiology
Humans
*Stem Cells/microbiology
*Host Microbial Interactions
Animals
*Host-Pathogen Interactions
Microbiota
Models, Biological
Regenerative Medicine/methods

@article {pmid40909339,
year = {2025},
author = {van Dorsten, RT and Breiman, RF},
title = {A landscape review with novel criteria to evaluate microbial drivers for cancer: priorities for innovative research targeting excessive cancer mortality in sub-Saharan Africa.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1625818},
pmid = {40909339},
issn = {2235-2988},
mesh = {Humans ; *Neoplasms/mortality/microbiology/epidemiology/etiology ; Africa South of the Sahara/epidemiology ; Microbiota ; Carcinogenesis ; },
abstract = {The escalating cancer burden in Sub-Saharan Africa (SSA), with projected doubling of incidence and mortality by 2040, necessitates innovative, cost-effective strategies for prevention, diagnosis, and treatment. While known infectious triggers like HPV, hepatitis viruses, and H. pylori account for an estimated 28.7% of cancers in SSA, the full scope of microbially-mediated oncogenesis remains underexplored. We examine existing data and formulate plausible hypotheses regarding the potential roles of additional infectious agents in cancer development within SSA. We explore mechanisms through which microbes may directly or indirectly contribute to oncogenesis, including the action of viral oncogenes, induction of chronic inflammation, mutational signatures, and the impact of immunosuppression, particularly in the context of HIV. Potential microbial triggers warrant further investigation, such as viruses (MMTV, CMV, polyomaviruses, SARS-CoV-2), bacteria (Fusobacterium nucleatum, Cutibacterium acnes, Salmonella Typhi), fungi (Candida, Aspergillus), parasites (Schistosoma japonicum and mansoni and Toxoplasma gondii) and the complex interplay with the microbiome. Given the significant challenges in establishing causation for microbial facilitators of cancer, with traditional postulates showing limited utility, we propose a refined set of criteria tailored to microbial oncogenesis, aiming to guide future research efforts. These criteria incorporate elements of both Koch's postulates and the Bradford Hill framework, adapted to address the unique characteristics of microbial interactions with human hosts. By leveraging existing knowledge and plausible causal relationships, and by implementing advanced experimental tools such as next-generation sequencing and multi-omics analyses, coupled with machine learning approaches and collaborative, multidisciplinary research, we propose to accelerate the identification of novel microbial links to cancer. This knowledge may pave the way for targeted interventions such as new approaches for screening and diagnosis, and strategies for prevention including vaccine development or modification of existing vaccines (or recommendations for immunization timing and population targets). While acknowledging the inherent complexities of studying polymicrobial interactions and the challenges of translating in vitro findings to human populations, this work aims to provide a framework for future research and intervention strategies to reduce the escalating cancer burden and address global inequities in SSA. The ultimate goal is to inform evidence-based public health policies and clinical practices that will improve cancer outcomes in this vulnerable region.},
}

Humans
*Neoplasms/mortality/microbiology/epidemiology/etiology
Africa South of the Sahara/epidemiology
Microbiota
Carcinogenesis

@article {pmid40909338,
year = {2025},
author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA},
title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629901},
pmid = {40909338},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; HIV-1/drug effects ; },
abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).

METHODS: Data from fecal shotgun metagenomics, plasma metabolome, cognitive (standardized neuropsychological test score covering 6 cognitive domains, NPZ-6), functional (neuropsychiatric symptoms) and neuroimaging assessments were obtained and evaluated in 18 participants before and after RMD administration, and at the study end (post-MAP follow-up) in the BCN02 trial.

RESULTS: Participants with neurocognitive impairment (Lower vs. Higher NPZ-6 score group) were enriched in bacterial species, including Desulfovibrio desulfuricans, Sutterella wadsworthensis and Streptococcus thermophilus, and showed higher 1,2-propanediol degradation microbial pathway levels, before RMD administration. A multi-omics profiling showed significant and positive correlations between these microbial features and lipid-related metabolic pathways, previously linked to neurological disorders (i.e., sphingolipid, ether lipid, and glycerophospholipid metabolism), in participants with neurocognitive impairment, before RMD administration. Three indices (microbial-, metabolite-based and combined) obtained from the discriminant features were assessed longitudinally, showing progressive similarities between NPZ-6 score groups over time. Furthermore, the three indices and related discriminant features correlated negatively with functional outcomes, such as quality of life and daily functioning, and positively with depression, stress and CNS-related symptoms before RMD administration, while these associations became less discernible at the subsequent timepoints.

CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolome
*HIV Infections/drug therapy/complications/microbiology
Male
Female
*Brain/physiopathology/physiology
Adult
Biomarkers/blood
Middle Aged
Feces/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
HIV-1/drug effects

@article {pmid40909218,
year = {2025},
author = {Tigrero-Vaca, J and Díaz, B and Gu, G and Cevallos-Cevallos, JM},
title = {Next-generation sequencing applications in food science: fundamentals and recent advances.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1638957},
pmid = {40909218},
issn = {2296-4185},
abstract = {Next-generation sequencing (NGS) has revolutionized food science, offering unprecedented insights into microbial communities, food safety, fermentation, and product authenticity. NGS techniques, including metagenetics, metagenomics, and metatranscriptomics, enable culture-independent pathogen detection, antimicrobial resistance surveillance, and detailed microbial profiling, significantly improving food safety monitoring and outbreak prevention. In food fermentation, NGS has enhanced our understanding of microbial interactions, flavor formation, and metabolic pathways, contributing to optimized starter cultures and improved product quality. Furthermore, NGS has become a valuable tool in food authentication and traceability, ensuring product integrity and detecting fraud. Despite its advantages, challenges such as high sequencing costs, data interpretation complexity, and the need for standardized workflows remain. Future research focusing on optimizing real-time sequencing technologies, expanding multi-omics approaches, and addressing regulatory frameworks is suggested to fully harness NGS's potential in ensuring food safety, quality, and innovation.},
}

@article {pmid40909168,
year = {2025},
author = {Siegwald, L and Cherta-Murillo, A and Christen, S and Boulangé, CL and Chou, CJ and Foata, F and Lahiry, A and Frézal, A and Giner, MP and Godin, JP and Sakwinska, O},
title = {The Impact of Low-Lactose, High Galacto-Oligosaccharides Milk on Gut Microbiome and Plasma Metabolome in Healthy Adults: A Randomized, Double-Blind, Controlled Clinical Trial Complemented by Ex Vivo Experiments.},
journal = {Current developments in nutrition},
volume = {9},
number = {9},
pages = {107506},
pmid = {40909168},
issn = {2475-2991},
abstract = {BACKGROUND: Galacto-oligosaccharides (GOS) intake has been linked to health benefits via modulation of the gut microbiome. Milk, where the majority of lactose is enzymatically converted to GOS (called here Novel or "N milk"), retains milk's nutritional value with reduced lactose and a high amount of prebiotic GOS.

OBJECTIVES: The aim of this study was to investigate the effect of N milk on the gut microbiome and related changes in health-related biomarkers, complemented by ex vivo fermentation experiments.

METHODS: In a 2-arm crossover, double-blind, randomized controlled clinical trial, 26 healthy adults consumed either N milk (containing 9 g GOS and 1.7 g of lactose per serving) or lactose-free milk (control), for 2 wk with a 2-wk washout period. Stool and fasting blood samples were collected at the start and the end of the intervention periods. Gut microbiome was analyzed using shotgun metagenomics, and metabolites using both targeted and untargeted methods. In addition, we tested lactose-free milk, N milk, and GOS in ex vivo colonic fermentation to obtain insights into the bacterial processing of substrates.

RESULTS: N milk intake led to a 3-fold increase in median gut bifidobacteria (P < 0.0001) and significant increases in plasma acetate, octanoic acid, β-alanine, and nicotinamide (all P < 0.05). Untargeted plasma metabolomics revealed a shift in amino acid metabolism, with an increase in 3-indole propionate, accompanied by a decrease in 2 uremic toxins, p-cresol sulfate, and indoxyl-sulfate (P < 0.05 without false discovery rate adjustment). Ex vivo fermentation experiments supported the results of the clinical study, whereby N milk increased bifidobacteria accompanied by higher production of short-chain fatty acids and a shift in microbial tryptophan metabolism, and indicated unique effects of N milk compared with GOS.

CONCLUSIONS: N milk resulted in a significant increase in gut bifidobacteria, along with changes in plasma metabolites previously associated with immune and metabolic health benefits.This study was registered at clinicaltrials.gov as NCT05207839.},
}

@article {pmid40909091,
year = {2025},
author = {Vineesh, A and Shah, S and Shah, K and Zaigham Hassan, M and Sapkota, A and Khadka, SR and Rizwanullah, F and Dare Ibrahim, A and Kanduri Hanumantharayudu, S and Kumar Makam Surendraiah, P and Ahmed, B and Gyullu, N},
title = {Exploring the Relationship Between Gut Health and Autoimmune Diseases: A Systematic Review and Meta-Analysis.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89300},
pmid = {40909091},
issn = {2168-8184},
abstract = {Autoimmune diseases (AIDs) are multifaceted, chronic illnesses characterized by immune dysregulation and systemic inflammation. Newer evidence has pointed a finger at the human gut microbiota, a trillion-fold population of microorganisms that inhabits the human GI tract, as a major influential modulator of immune reactivity and a significant contributor to autoimmune pathogenesis. This systematic review will seek to address how the literature correlates with systematic changes in the gut microbiota in AIDs as well as explore mechanistic associations with biological processes like intestinal permeability and modulation of the immune system, coupled with determining the effectiveness of microbiota-directed interventions. An extensive literature search was conducted in PubMed, Embase, Cochrane Central, and Web of Science, involving the availability of studies until May 2025. The eligible studies included observational studies, randomized controlled trials, and relevant mechanistic research regarding autoimmune diseases and alterations of the gut microbiome or administered interventions. Data extraction and risk of bias (ROB) assessments were performed by two independent reviewers, and a narrative synthesis with an illustrative meta-analysis was applied. Inclusion criteria were met by 10 studies, encompassing various autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), multiple sclerosis (MS), type 1 diabetes mellitus (T1DM), autoimmune thyroid diseases (AITDs), and psoriasis. Familiar patterns of microbiome dysbiosis were identified, such as a reduction in microbial diversity, increased intestinal permeability, and the expansion of pro-inflammatory species like Ruminococcus gnavus. Dietary interventions, fecal microbiota transplantation, and probiotics demonstrated positive effects on clinical outcomes and immune measures across multiple studies. The meta-analysis revealed that microbiota-directed interventions significantly improved disease activity and immune response markers in AIDs, indicating a robust link between gut microbiota composition and autoimmune pathology. In autoimmune disorders, gut microbiota is a key factor in immunopathology. Gut biology as an adjunct interventional strategy provides potential in managing these diseases. Additional studies are required to help standardize methods and identify microbial targets specific to diseases that can then be addressed through therapeutic interventions.},
}

@article {pmid40908980,
year = {2025},
author = {Keeler, CE and Oguguo, E and Goodwin, CR and Goertz, C},
title = {The Role of Nutrition in Low Back Pain: A Narrative Review and Clinical Implications.},
journal = {American journal of lifestyle medicine},
volume = {},
number = {},
pages = {15598276251375398},
pmid = {40908980},
issn = {1559-8284},
abstract = {Low back pain is a pervasive global public health problem. As with other chronic non-communicable diseases, dietary intervention can improve clinical outcomes and reduce health care costs. Pharmacologic and non-pharmacologic treatments are included in non-invasive treatment clinical practice guidelines. Nutrition recommendations can also be added. This review summarizes existing information on nutrition and low back pain, identifies areas for further investigation, and proposes a role for dietary recommendations in treatment and prevention from a public health and patient care perspective. Nutritional goals for decreasing low back pain include maintaining a healthy weight, following an anti-inflammatory diet, optimizing micronutrient intake, and promoting gut microbiome health. Adherence to nutrition and health recommendations is influenced by social determinants of health, including neighborhood design, structural racism, access to healthy food, socioeconomic status, and educational level. Achieving nutritional health equity must be a top priority to reduce existing health disparities. Future research on the role of nutrition in low back pain, including optimal dietary patterns, should focus on developing recommendations to be integrated into an interdisciplinary approach to low back pain.},
}

@article {pmid40908830,
year = {2025},
author = {Yamlahi, YE and Remmal, I and Maurady, A and Britel, MR and Bakali, AH and Mokhtar, NB and Galiatsatos, I and Stathopoulou, P and Tsiamis, G},
title = {Characterization of the olive fly (Bactrocera oleae) microbiome across diverse geographic regions of Morocco.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70126},
pmid = {40908830},
issn = {1744-7917},
support = {22662//International Atomic Energy Agency/ ; },
abstract = {The olive fruit fly (Bactrocera oleae) is a significant pest threatening olive production worldwide. Bactrocera oleae relies on symbiotic bacteria for nutrition, development, and adaptation to its environment. Among these, Candidatus Erwinia dacicola is the most dominant symbiont and plays a key role in the fly's physiology and ecological adaptation. Understanding the dynamics between B. oleae, Ca. E. dacicola, and other components of the B. oleae microbiome is essential for developing effective targeted area-wide pest management strategies. This study aims to leverage full 16S rRNA gene sequencing to enhance the characterization of microbiome diversity in wild B. oleae populations from different regions in Morocco: Ouezzane, Rabat, Tanger, Errachidia, and Beni-Mellal. The results revealed distinct microbiome compositions influenced by geographic locations, with Candidatus Erwinia dacicola as the dominant symbiont, followed by Erwinia persicina as a secondary contributor. Other bacterial taxa, including Asaia bogorensis, were also identified, highlighting the functional diversity within the olive fly microbiome. These findings provide insights into the microbial ecology of B. oleae, contributing to the development and enhancement of sustainable pest control strategies.},
}

@article {pmid40908816,
year = {2025},
author = {Tan, Z and Huang, Y and Fu, S and Li, H and Gong, C and Lv, D and Yang, C and Wang, J and Ding, M and Wang, H},
title = {Construction of a gene-metabolite-microbiome regulatory network reveals novel therapeutic targets in bladder cancer through multi-omics analysis.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2553220},
doi = {10.1080/07853890.2025.2553220},
pmid = {40908816},
issn = {1365-2060},
mesh = {Humans ; *Urinary Bladder Neoplasms/genetics/microbiology/metabolism/drug therapy ; *Microbiota/genetics ; *Gene Regulatory Networks ; Exome Sequencing ; Male ; Female ; Metabolomics/methods ; Single-Cell Analysis ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Multiomics ; },
abstract = {BACKGROUND: Bladder cancer (BLCA) is a prevalent malignancy with substantial consequences for patient health. This study aimed to elucidate the underlying mechanisms of BLCA through integrated multi-omics analysis.

METHODS: Tumor and adjacent tissues from BLCA patients underwent transcriptomic, whole-exome sequencing, metabolomic, and intratumoral microbiome analyses. These data were integrated with public datasets to identify key genes, metabolites, and microorganisms. Molecular subtypes were defined by key gene expression and compared for pathways, immune profiles, mutations, immunotherapy response, and drug sensitivity. Prognostic relevance was validated in external cohorts. Single-cell sequencing was applied to reveal cellular localization of key genes.

RESULTS: Three key genes (AHNAK, CSPG4, NCAM1), 90 metabolites, and two microbes (Sphingomonas koreensis, Rhodospirillaceae) were identified. Key genes negatively correlated with metabolites but not with microbes. BLCA samples were classified into two molecular clusters with distinct ECM organization, metabolic features, immune checkpoint expression, and therapeutic sensitivity. NCAM1 correlated positively with γδ T cells and negatively with M0 macrophages. Single-cell analysis revealed nine major cell types, with fibroblasts displaying the highest expression of key genes, particularly elevated AHNAK in specific fibroblast subtypes. Drug prediction and docking identified candidate compounds targeting these genes with stable binding potential.

CONCLUSION: This comprehensive multi-omics analysis links key genes, metabolites, and microbes to BLCA pathogenesis. Fibroblasts emerge as central regulators, while identified gene-metabolite interactions and microbial associations provide novel insights into tumor heterogeneity. These findings highlight potential biomarkers and therapeutic targets to support precision treatment in BLCA.},
}

Humans
*Urinary Bladder Neoplasms/genetics/microbiology/metabolism/drug therapy
*Microbiota/genetics
*Gene Regulatory Networks
Exome Sequencing
Male
Female
Metabolomics/methods
Single-Cell Analysis
Transcriptome
Gene Expression Regulation, Neoplastic
Multiomics

@article {pmid40908772,
year = {2025},
author = {Faysal, M and Zehravi, M and Sutradhar, B and Al Amin, M and Shanmugarajan, TS and Arjun, UVNV and Ethiraj, S and Durairaj, A and Dayalan, G and Ahamad, SK and Rab, SO and Raman, K and Emran, TB},
title = {The Microbiota-Gut-Brain Connection: A New Horizon in Neurological and Neuropsychiatric Disorders.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {9},
pages = {e70593},
doi = {10.1111/cns.70593},
pmid = {40908772},
issn = {1755-5949},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mental Disorders/microbiology/metabolism/therapy ; *Nervous System Diseases/microbiology/metabolism/therapy ; *Brain/metabolism ; Animals ; Dysbiosis ; *Brain-Gut Axis/physiology ; Probiotics ; },
abstract = {INTRODUCTION: The microbiota-gut-brain axis (MGBA), a complex two-way connection between the gut microbiota and the brain, has become a key regulator of neurological and neuropsychiatric disorders. Neurological disorders and gut microbiota dysbiosis are linked to these diseases. Changes in gut microbiota can lead to neurotransmitter imbalances, oxidative stress, and neuroinflammation. Gut dysbiosis may contribute to the development of diseases such as depression, autism, schizophrenia, bipolar disorder, Parkinson's disease, Alzheimer's disease, dementia, multiple sclerosis, epilepsy, anxiety, and autism spectrum disorders through immunological regulation, neuroinflammation, and neurotransmitter metabolism changes.

METHOD: This review systematically sourced articles related to microbiota gut brain axis, neurological disorders, neuropsychiatric disorders and clinical studies from major medical databases, including Scopus, PubMed, and Web of Science.

RESULTS: This review explores the molecular processes underlying MGBA interactions, including vagus nerve signaling, systemic immunological responses, and metabolites produced by microorganisms. The discussion explores the potential of microbiome-targeted treatments like fecal microbiota transplantation, probiotics, and prebiotics as effective treatment methods. The comprehension of the MGBA can revolutionize neurology and psychiatry, introducing innovative diagnostic and therapeutic approaches. Multiple elements, including diet, metabolism, age, stress, and medications, shape the human gut microbiota, and intestinal imbalances can lead to CNS diseases. The MGBA interacts with gut bacteria, and gut dysbiosis is associated with neurological disorders.

CONCLUSIONS: The review demonstrates the correlation between gut microbiota and neurologically associated diseases, highlighting its importance in neurogenesis, mental development, emotions, and behaviors. MGBA, mediated by microbial metabolites, affects brain function and neuroinflammation. Interventions like fetal microbiota transplantation, probiotics, and prebiotics can improve microbial balance, but more clinical research is needed.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mental Disorders/microbiology/metabolism/therapy
*Nervous System Diseases/microbiology/metabolism/therapy
*Brain/metabolism
Animals
Dysbiosis
*Brain-Gut Axis/physiology
Probiotics

@article {pmid40908699,
year = {2025},
author = {Romi, and Sharma, D and Sharma, A and Gupta, P},
title = {A New Era of Therapeutics: Innovation in the Treatment of Rheumatoid Arthritis.},
journal = {Recent advances in anti-infective drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127724344382299250818070846},
pmid = {40908699},
issn = {2772-4352},
abstract = {Rheumatoid arthritis is a chronic autoimmune disease with joint destruction and chronic inflammation symptoms. Conventional therapy focuses on the prevention of the progression of the disease and management of symptoms, rather than curing the disease. Emerging therapies have been developed to cure the disease, which combines conventional therapies with a novel drug delivery system. Novel therapies have better bioavailability, which is marked by reduced adverse reactions. In the following article, some of the emerging therapies focused on the notable advancement in the procurement of the RA include microRNA alteration, helper T-cell inhibition, drug repurposing, targeting sites for interleukins, and blocking of signaling pathways. Beyond pharmacological intervention, emerging therapies explore the modulation of the microbiome, epigenetic regulation, and the manipulation of immune tolerance mechanisms. These therapies offer hope for better disease control and potential advantages for future betterment.},
}

@article {pmid40908690,
year = {2025},
author = {Singh, H and Kumar, R and Mazumder, A},
title = {Unlocking the Potential of Polysaccharides for the Treatment of Lung Cancer.},
journal = {Anti-cancer agents in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715206395910250816110857},
pmid = {40908690},
issn = {1875-5992},
abstract = {BACKGROUND: Lung cancer remains a leading cause of cancer-related deaths worldwide, with its incidence continuing to rise. Despite advancements in clinical treatments, their effectiveness is often restricted, emphasizing the need for novel therapeutic strategies. Natural products have long been explored for drug development, and among them, polysaccharides have gained significant attention due to their biocompatibility, biodegradability, and multiple biological functions.

METHODS: A comprehensive review examined contemporary research on the anticancer properties of natural polysaccharides, focusing specifically on their effects in lung cancer. The analysis included studies investigating their influence on cancer cell growth, immune system modulation, and therapeutic outcomes. Evidence from laboratory (in vitro), animal (in vivo), and clinical studies was evaluated to provide a comprehensive overview of their potential role in lung cancer management.

RESULTS: Findings from recent studies indicate that polysaccharides can effectively inhibit the proliferation of lung cancer cells, thereby slowing tumor development. These compounds also appear to enhance immune responses by activating various immune cells and regulating cytokine production. Furthermore, polysaccharides have been shown to positively affect the gut microbiota, which may contribute to improved drug efficacy and a reduction in resistance to chemotherapy.

DISCUSSION: The evidence suggests that natural polysaccharides exert multifaceted effects in the context of lung cancer treatment. Their ability to directly suppress tumor growth, modulate the immune system, and interact with the gut microbiome positions them as promising adjuncts to existing therapies. However, the precise molecular mechanisms underlying these effects are not yet fully understood, and variability in study designs warrants cautious interpretation of the results.

CONCLUSION: Natural polysaccharides represent a promising complementary approach for lung cancer therapy, given their potential to inhibit tumor progression, enhance immune function, and improve the effectiveness of conventional drugs. Continued research is essential to fully elucidate their mechanisms of action and to translate these findings into effective clinical interventions.},
}

@article {pmid40908532,
year = {2025},
author = {Wei, M and Mehravar, S and Leite, G and Naji, P and Barlow, GM and Hosseini, A and Rashid, M and Sanchez, M and Fajardo, CM and Pimentel, M and Mathur, R},
title = {Relationship between hypothyroidism, risk of small intestinal bacterial overgrowth, and duodenal microbiome alterations.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf495},
pmid = {40908532},
issn = {1945-7197},
abstract = {CONTEXT: There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these two conditions is not fully elucidated.

OBJECTIVE: We evaluate the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.

DESIGN AND OUTCOME MEASURES: Duodenal aspirates from REIMAGINE study subjects with a history of hypothyroidism (hypothyroid group, N=49) and controls (N=323) underwent 16S rRNA sequencing (MiSeq, Illumina); a subset also underwent metagenomic sequencing (NovaSeq6000, Illumina). Separately, the TriNetX Analytics platform was used to evaluate ten-year cumulative incidences and relative risk [RR] of developing SIBO in subjects with hypothyroidism (unspecified etiology, HUE), and a subset with autoimmune thyroiditis, vs. propensity score matched (PSM) control groups.

RESULTS: Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs. controls (15.17%). In the TriNetX analysis, ten-year cumulative incidences of SIBO were higher in HUE (RR=2.20) and autoimmune thyroiditis (RR=2.40) subjects vs. matched controls. However, these risks appeared to be mitigated both in HUE (RR=0.33) and autoimmune thyroiditis (RR=0.78) subjects taking levothyroxine. Analyzing the duodenal microbiome, genus Neisseria was part of the core microbiome in the hypothyroid group (Hypo+/SIBO-, Hypo+/SIBO+) but not in non-hypothyroid subjects (Hypo-/SIBO-, Hypo-/SIBO+). Increased prevalence of Gram-negative coliforms occurred in both SIBO+ groups, but Escherichia/Shigella formed part of the core in non-hypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).

CONCLUSION: These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism which may be ameliorated by treatment, and may involve specific Gram-negative coliforms.},
}

@article {pmid40908531,
year = {2025},
author = {Faisal, and Sekhar, SRM and Anurag, DS and Kumar, V and Shetty, D and Sharma, D},
title = {Deciphering Gut Microbiome Dynamics in Irritable Bowel Syndrome Using Deep Learning.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70153},
doi = {10.1111/nmo.70153},
pmid = {40908531},
issn = {1365-2982},
abstract = {PURPOSE: This work delves into the critical role of the human gut microbiome in health and disease, emphasizing its influence on a range of physiological processes and its connection to conditions such as irritable bowel syndrome (IBS). The microbiome is made up of a very large and complicated group of microorganisms that have big effects on metabolic and immune functions. This makes it an interesting area for researching new ways to diagnose and treat diseases. Analyzing this data introduces substantial challenges due to its high dimensionality, intricate microbial interactions, and significant inter-individual variability.

METHODS: The above factors demand the application of sophisticated machine learning techniques that can efficiently manage and interpret such complex, high-dimensional data. The XGBoost, RandomForest, Logistic Regression, LightGBM, and a deep neural network (DNN) are specifically tailored for this work. Each model's implementation is meticulously designed to extract meaningful patterns from the microbiome data with the required preprocessing by focusing on achieving high accuracy, sensitivity, and specificity in disease classification. The models are implemented using Python's libraries and are evaluated through rigorous cross-validation on a comprehensive dataset of microbiome profiles to ensure robustness and reliability.

RESULTS: A comparison study is done to find out what each model does well and what it does not do so well. The DNN's dense layered neurocomputing pattern recognition skills make it very good at dealing with the complexity of microbiome data, resulting in an accuracy of 92.79%.

CONCLUSION: This study not only adds to our knowledge of how the microbiome affects health, but it also pushes the limits of diagnostic methods. By using cutting-edge deep machine learning innovations in biomedical research, we may be able to improve health outcomes around the world.},
}

@article {pmid40907861,
year = {2025},
author = {Frizon, L and Rocchetti, TT and Frizon, A and de Alcântara, RJA and Hofling-Lima, AL and de Paiva, CS and Gomes, JÁP},
title = {Ocular bacterial microbiome analysis by next-generation sequencing in patients with Stevens-Johnson syndrome and Sjögren's disease: associations with dry eye indices.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110622},
doi = {10.1016/j.exer.2025.110622},
pmid = {40907861},
issn = {1096-0007},
abstract = {The ocular surface microbiome plays a crucial role in maintaining immune homeostasis, and its disruption may contribute to mucosal inflammation and autoimmunity. This pilot exploratory study investigated and compared the ocular surface bacterial microbiome in patients with Stevens-Johnson syndrome (SJS), Sjögren's disease (SjD), and healthy controls using next-generation sequencing (NGS) and correlated these findings with dry eye parameters. Conjunctival swabs were collected from sixteen individuals: ten with SJS, three with SjD, and three healthy controls. Dry eye parameters were employed to evaluate the dry eye disease. Microbiome profiles were determined by the NGS of the 16S V3-V4 region and analyzed using the SILVA database. The microbiome exhibited notable differences at the genus level among the SJS group. Specifically, the abundance of Staphylococcus was significantly lower in the SJS group compared to both the SjD and healthy controls (p = 0.04). In contrast, increased levels of Streptococcus and Corynebacterium were associated with higher scores on the Dry Eye Disease of Dry Eye Workshop (DED DEWS score) (p = 0.003) and the Ocular Surface Disease Index (OSDI) score (p = 0.01), respectively. Conversely, elevated levels of Cutibacterium and Pseudomonas were associated with more severe dry eye, as evidenced by lower Schirmer I test results (p = 0.003) and tear break-up time (TBUT) values (p = 0.05). In contrast, the ocular microbiome of SjD patients was similar to that of healthy controls. In conclusion, patients with SJS exhibited distinct changes in the ocular microbiota, with specific bacterial genera associated with dry eye severity, suggesting a potential role for microbial alterations in the ocular surface inflammation.},
}

@article {pmid40907803,
year = {2025},
author = {Nkansah, EO and Xu, B and Lan, Y and Zafar, MI},
title = {Positioning Nutrigenomics and Nutrigenetics within the Framework of Male Infertility Exploration.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {},
number = {},
pages = {109043},
doi = {10.1016/j.reprotox.2025.109043},
pmid = {40907803},
issn = {1873-1708},
abstract = {Male infertility, a complex result of genetic, environmental, and lifestyle factors, has gained significant focus in contemporary medical research. The intricate interplay between genetics, nutrition, and male fertility is crucial for understanding the complex mechanisms that underlie male reproductive health. The twenty-first century has seen a paradigm shift in medicine, where holistic personalized medical care is posited to be ideal and effective. In this regard, this narrative review explored how the convergence of dietary habits and genetic predispositions influence male fertility in the context of predictive, preventive, and personalized medicine. This review explored the evolving landscape of genetic insights into male infertility, creating awareness of their possible engagement as genetic predictors for idiopathic male infertility. It also dissects the roles of nutrigenomics and nutrigenetics in shaping preventive male reproductive medicine strategies through distinguishing the influence of dietary components on genetic expression and further elucidating how epigenetic alterations, influenced by dietary components, impact male fertility, potentially imparting transgenerational effects. Furthermore, this review offers potential personalized reproductive remedies in the form of functional and super foods, gut microbiome enhancers, redox homeostasis and proposes personalized nutrition as an intervention with high prospects in the context of improving male fertility.},
}

@article {pmid40907680,
year = {2025},
author = {Ma, X and Zhang, J and Wang, Y and Shi, L and Zhu, Y and Wang, L and Li, J and He, S},
title = {Association between microplastics exposure and gut microbiota and metabolites in older adults: A cross-sectional study.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122735},
doi = {10.1016/j.envres.2025.122735},
pmid = {40907680},
issn = {1096-0953},
abstract = {BACKGROUND: Microplastics (MPs) pollution is a global issue. Due to long-term accumulation and physiological decline, older adults may be more susceptible to its effects. This study aims to evaluate the associations between MPs and the gut microbiota and metabolites in older adults.

METHOD: During the 2024 follow-up of the Ningxia Older Mental Health Cohort, 45 fecal samples were collected. MP detection was performed using laser direct infrared imaging spectrometer (LDIR), and principal coordinates analysis (PCoA) was used to assess microbial community similarity. Wilcoxon tests were used for intergroup comparisons of microbial dysbiosis index (MDI), gut microbiome health index (GMHI), and microbial abundance. Differential metabolites were screened using the orthogonal partial least squares discriminant analysis (OPLS-DA) model and univariate analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database was used for pathway annotation. Bland-Altman analysis evaluated the consistency between fecal MP detection counts and the plastic exposure score (PES) from questionnaires.

RESULTS: The average count of MPs in feces was 70.10 particles/g, primarily consisting of polyvinyl chloride (PVC), butadiene rubber (BR), and polyethylene (PE). MP exposure may affect the beta diversity, MDI, and GMHI in older adults. Furthermore, changes in the abundance of certain species in the gut microbiota, such as Klebsiella and Escherichia-Shigella, and levels of metabolites, such as taurine and γ-aminobutyric acid (GABA), were associated with MP exposure. A total of 30 KEGG pathways were significantly enriched, with the primary pathways including taurine and hypotaurine metabolism, and ligand-receptor interaction. MP detection counts show good consistency with PES.

CONCLUSION: MP exposure is associated with changes in the characteristics of gut microbiota, microbial abundance, and metabolite levels. PES may serve as a suitable alternative tool for assessing plastic exposure in large populations.},
}

@article {pmid40907381,
year = {2025},
author = {Cini, E and Vinciarelli, G and Siciliano, S and Del Castello, G and Dreassi, E and Poggialini, F and Vagaggini, C and Taddei, M and Battistuzzi, G and Castagnetti, A and Viciani, E and Salvini, L and Sidoti, A and Alibrandi, S and Giannini, G},
title = {Fluoromethylcarnitine, a novel inhibitor of trimethylamine levels in trimethylaminuria and trimethylamine N-oxide related disorders.},
journal = {European journal of medicinal chemistry},
volume = {300},
number = {},
pages = {118073},
doi = {10.1016/j.ejmech.2025.118073},
pmid = {40907381},
issn = {1768-3254},
abstract = {Excessive production of trimethylamine (TMA) by the gut microbiota leads to increased concentrations of TMA or trimethylamine N-oxide (TMAO) in the bloodstream, which is associated with health risks. High levels of TMAO have been linked to cardiovascular disease, inflammation and other health problems. In addition, people affected by a genetic deficiency of the liver enzyme FMO3, which oxidises TMA to TMAO, suffer from trimethylaminuria (TMAU), a rare disorder caused by mutations in the Fmo3 gene, in which the body odour resembles that of rotting fish, leading to significant discomfort and social isolation. We report here on (R)-N-fluoromethylcarnitine (FCAR), the first inhibitor of TMA production that acts without altering the microbiome and has favourable pharmacokinetic properties. We also tested FCAR in an animal model of trimethylaminuria (TMAU) using mice with a knock-out for the Fmo3 gene. We observed that FCAR reduced TMA levels in the blood and urine of these mice. No weight loss was observed in the animals, demonstrating the low toxicity of FCAR and making it a potential candidate for clinical development for the treatment of trimethylaminuria (TMAU) and other TMA-related disorders.},
}

@article {pmid40907265,
year = {2025},
author = {Zhang, Y and Zhou, Z and Li, Y and Xu, M and Li, Y and Yang, Y and Hu, X and Wang, X and Yi, H and Wu, X},
title = {Clostridial-dominated gut microbiota promotes 7α-dehydroxylation of obeticholic acid to lithocholic acid in cholestasis treatment.},
journal = {Biochemical and biophysical research communications},
volume = {782},
number = {},
pages = {152565},
doi = {10.1016/j.bbrc.2025.152565},
pmid = {40907265},
issn = {1090-2104},
abstract = {Obeticholic acid (OCA) is a potent farnesoid X receptor (FXR) agonist used in the treatment of liver diseases associated with cholestasis, such as primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). However, its clinical utility is limited by dose-dependent hepatotoxicity, and the precise mechanism underlying OCA toxicity remains unclear. In this study, we investigated the mechanistic link between cholestasis-induced gut dysbiosis and OCA-associated hepatotoxicity. Cholestasis induces a significant shift in the gut microbiota composition, leading to a dysbiotic state dominated by the genera Clostridium, Bacteroides, and Lactobacillus. Crucially, the upregulation of bile acid inducible (bai) operon-encoded 7α-dehydroxylase in gut microbiota potently drives the metabolic conversion of OCA to lithocholic acid (LCA), a highly hepatotoxic secondary bile acid. This accelerated biotransformation of OCA to LCA provides a mechanistic explanation for the dose-dependent hepatotoxicity observed with OCA treatment, thereby elucidating the underlying cause of OCA-induced liver injury. These findings establish a direct causal link between cholestasis-driven gut dysbiosis, enhanced microbial 7α-dehydroxylation, and the bioactivation of OCA to its toxic metabolite, LCA. Consequently, this study underscores the gut microbiome as a critical determinant governing both the therapeutic efficacy and the adverse toxicity profile of bile acid-based therapeutics like OCA. Importantly, the results suggest that targeted modulation of the gut microbiota composition represent promising therapeutic strategies to mitigate OCA-associated hepatotoxicity and improve its clinical safety profile.},
}

@article {pmid40907025,
year = {2025},
author = {Siddiqui, NY and Bradley, MS},
title = {Updates in Clinical Management of Recurrent Urinary Tract Infections.},
journal = {Obstetrics and gynecology},
volume = {},
number = {},
pages = {},
pmid = {40907025},
issn = {1873-233X},
abstract = {Urinary tract infections (UTIs) are common and burdensome in women. Here, we discuss challenges with our current models of care and how evolving insights into the female urogenital microbiome have advanced the understanding of how we diagnose, treat, and prevent recurrent UTIs in nonpregnant adult women. Traditional care models attribute recurrent UTIs mainly to gastrointestinal sources, resulting in significant emphasis on eradicating pathogens with potential overreliance on antibiotics. Evidence now shows that the bladder harbors a complex microbiome, with interactions between the urinary and vaginal environments and immune mechanisms at the bladder mucosal surface influencing infection susceptibility. Thus, in updated models of care, more emphasis is placed on enhancing the protective microbiome. This may be especially important in postmenopausal women, who experience microbiome shifts that increase vulnerability to recurrent infections, underscoring the role of estrogen therapy and microbiome-supportive interventions. Updated treatment approaches emphasize antimicrobial stewardship, advocating for confirmation of the diagnosis and delayed antibiotic initiation when safe, and judicious use of antibiotics for symptom relief. Prevention strategies highlight the importance of vaginal estrogen, methenamine salts, and other supplements rather than exclusive reliance on prophylactic antibiotics. Ongoing research into emerging therapies such as UTI vaccines and bacteriophage drugs may further decrease our reliance on antibiotics in the future. This clinical update underscores the need for individualized care plans that balance effective infection management while minimizing antibiotic-related harms, emphasizing a holistic, microbiome-centered approach to recurrent UTI prevention and treatment.},
}

@article {pmid40906895,
year = {2025},
author = {Berg, G and Toledo, GV and Schierstaedt, J and Hyöty, H and Adi Wicaksono, W},
title = {Linking the edible plant microbiome and human gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2551113},
doi = {10.1080/19490976.2025.2551113},
pmid = {40906895},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Plants, Edible/microbiology ; *Vegetables/microbiology ; Fruit/microbiology ; Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; },
abstract = {The edible plant microbiome, which includes microbes in raw-eaten plants, has been recently recognized as a vehicle delivering microbes to the gut. Fruits and vegetables can carry thousands to billions of microorganisms with diverse genetic capacities on each serving. Since the 'edible plant microbiome' concept was introduced in 2014, notable progress has been made in understanding its microbial diversity, factors influencing it, functional traits and biomarkers, and its interconnection with the human gut microbiome. The discovery of the link between microbes in plants consumed raw and the gut microbiome establishes a possible continuum from farm to fork and health.},
}

Humans
*Gastrointestinal Microbiome
*Plants, Edible/microbiology
*Vegetables/microbiology
Fruit/microbiology
Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Tract/microbiology

@article {pmid40906858,
year = {2025},
author = {Pountain, AW and Yanai, I},
title = {Dissecting microbial communities with single-cell transcriptome analysis.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6764},
pages = {eadp6252},
doi = {10.1126/science.adp6252},
pmid = {40906858},
issn = {1095-9203},
mesh = {*Single-Cell Analysis/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; *Gene Expression Profiling/methods ; *Transcriptome ; *Bacteria/genetics ; *Microbiota/genetics ; Interspersed Repetitive Sequences ; Anti-Bacterial Agents/pharmacology ; Single-Cell Gene Expression Analysis ; },
abstract = {Revealing insights into the function of microbial communities requires moving beyond measuring bulk taxonomic composition to detecting interactions between subpopulations. Following the transformative impact of single-cell gene expression profiling techniques on numerous fields of human biology, recent years have seen increased application to microbes. We review progress in the development of these techniques and discuss challenges in applying them to microbial communities. We highlight applications for dissecting the microbiome in human health and disease that reveal functional heterogeneity within gut communities, antibiotic responses, and the dynamics of mobile genetic elements. As single-cell gene expression technologies continue to develop, they are becoming ever more essential for examining and modulating the role of microbial communities in clinical and wider environments.},
}

*Single-Cell Analysis/methods
Humans
*Gastrointestinal Microbiome/genetics
*Gene Expression Profiling/methods
*Transcriptome
*Bacteria/genetics
*Microbiota/genetics
Interspersed Repetitive Sequences
Anti-Bacterial Agents/pharmacology
Single-Cell Gene Expression Analysis

@article {pmid40906521,
year = {2025},
author = {Selten, G and Gómez-Repollés, A and Lamouche, F and Radutoiu, S and de Jonge, R},
title = {SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001461},
pmid = {40906521},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The plant root microbiome is a complex community shaped by interactions among bacteria, the plant host and the environment. Synthetic community (SynCom) experiments help disentangle these interactions by inoculating host plants with a representative set of culturable microbial isolates from the natural root microbiome. Studying these simplified communities provides valuable insights into microbiome assembly and function. However, as SynComs become increasingly complex to better represent natural communities, bioinformatics challenges arise. Specifically, accurately identifying and quantifying SynCom members based on, for example, 16S rRNA amplicon sequencing becomes more difficult due to the high similarity of the target amplicon, limiting downstream interpretations. Here, we present SynCom Fingerprinting (SyFi), a bioinformatics workflow designed to improve the resolution and accuracy of SynCom member identification. SyFi consists of three modules: the first module constructs a genomic fingerprint for each SynCom member based on its genome sequence and, when available, raw genomic reads, accounting for both copy number and sequence variation in the target gene. The second module extracts the target region from this genomic fingerprint to create a secondary fingerprint linked to the relevant amplicon sequence. The third module uses these fingerprints as a reference to perform pseudoalignment-based quantification of SynCom member abundance from amplicon sequencing reads. We demonstrate that SyFi outperforms standard amplicon analysis by leveraging natural intragenomic variation, enabling more precise differentiation of closely related SynCom members. As a result, SyFi enhances the reliability of microbiome experiments using complex SynComs, which more accurately reflect natural communities. This improved resolution is essential for advancing our understanding of the root microbiome and its impact on plant health and productivity in agricultural and ecological settings. SyFi is available at https://github.com/adriangeerre/SyFi.},
}

*Microbiota/genetics
*Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Computational Biology/methods
High-Throughput Nucleotide Sequencing
*DNA Fingerprinting/methods
Sequence Analysis, DNA/methods

@article {pmid40906440,
year = {2025},
author = {Faas, MM and Wekema, L and van Loo-Bouwman, CA and Weiss, GA and Hung, WL and de Haan, BJ and Smink, AM},
title = {Bifidobacterium animalis subsp. Lactis BL-99 Improves Maternal and Fetal Immune Responses and Pregnancy Outcomes in Pregnant Antibiotics-Treated Mice.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70220},
doi = {10.1002/mnfr.70220},
pmid = {40906440},
issn = {1613-4133},
abstract = {The maternal gut microbiome is involved in adapting immune responses to the presence of the semiallogeneic foetus. We have previously shown that antibiotics-induced gut dysbiosis, alterations in the maternal immune response and decreased foetal and placental weight. Here, we tested whether Bifidobacterium animalis subsp. lactis BL-99 (BL-99) could improve antibiotics-induced gut dysbiosis, maternal immune responses and foetal and placental weight. To do so, pregnant mice received antibiotics in their drinking water (day 9-16) and BL-99 via oral gavage (day 9-18). After sacrifice (day 18) immune responses were measured using flowcytometry. BL-99 increased placental weight in antibiotics-treated pregnant mice. BL-99 did not significantly change the maternal microbiome, but improved maternal immune responses by decreasing splenic Th1 cells and Treg cells, and increasing FoxP3/RoRγT double-positive cells in the Peyer's patches to levels observed in control pregnant mice. BL-99 also improved monocyte subsets and activation status. Additionally, BL-99 changed foetal monocyte subsets and activational status and increased foetal splenic Th cells. We thus showed that the effect of antibiotics treatment on immune cells and placental weight was mitigated by supplementation of BL-99. We suggest that pregnancy complications associated with a disturbed microbiome and immune responses, such as preeclampsia or obese pregnancies, could benefit from BL-99 supplementation. This should be tested in future studies.},
}

@article {pmid40906400,
year = {2025},
author = {Zeng, Q and Wang, Z and Shen, Z and Li, W and Luo, K and Qin, Q and Li, S and Gu, Q},
title = {Microbiome Diversity and Dynamics in Lotus-Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081092},
pmid = {40906400},
issn = {2079-7737},
support = {2023YFD2400902//National Key Research and Development Program of China/ ; 2023YFD2401605//National Key Research and Development Plan Program/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; },
abstract = {The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.},
}

@article {pmid40906396,
year = {2025},
author = {Makwarela, TG and Seoraj-Pillai, N and Nangammbi, TC},
title = {Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081086},
pmid = {40906396},
issn = {2079-7737},
abstract = {Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host's genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk-microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science.},
}

@article {pmid40906320,
year = {2025},
author = {Ilozumba, MN and Gomez, MF and Lin, T and Himbert, C and Round, JL and Zac Stephens, W and Warby, CA and Hardikar, S and Li, CI and Figueiredo, JC and Damerell, V and Fillmore, GC and Pickron, B and Toriola, AT and Shibata, D and Holowatyj, AN and Kahlert, C and Sankar, K and Siegel, EM and Jedrzkiewicz, J and Gigic, B and Byrd, DA and Ose, J and Ulrich, CM},
title = {Pre-surgery gut microbial diversity and abundance are associated with post-surgery onset of cachexia in colorectal cancer patients: the ColoCare Study.},
journal = {Cancer causes & control : CCC},
volume = {},
number = {},
pages = {},
pmid = {40906320},
issn = {1573-7225},
support = {U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; U01 CA206110, R01 CA189184, R01 CA207371, R01 CA211705, R01 CA254108//National Institutes of Health/ National Cancer Institute/ ; 01KD2101D//the German Ministry of Education and Research project PerMiCCion/ ; 01KD2101D//the German Ministry of Education and Research project PerMiCCion/ ; },
abstract = {BACKGROUND: Cachexia accounts for about 20% of all cancer-related deaths and it is indicative of poor prognosis and progressive functional impairment. The role of the gut microbiome in the development of cachexia in colorectal cancer (CRC) patients has not been established.

METHODS: Pre-surgical stool samples from n = 103 stage I-III CRC patients in the ColoCare Study were analyzed using 16S rRNA gene sequencing (Illumina) to characterize fecal bacteria. We calculated estimates of alpha- and beta-diversity and a priori- and exploratory-selected bacterial relative abundance. Using Fearon criteria, cachexia onset at 6 months post-surgery was defined as > 5% weight loss over the past 6 months and/or body mass index (BMI) of < 20 kg/m[2] and weight loss of > 2%. Associations of microbial metrics with cachexia onset were estimated using multivariable logistic regression models.

RESULTS: Higher alpha-diversity was positively associated with cachexia onset, with stronger associations in females, patients < 65 years, those receiving adjuvant treatment, consuming high fiber, or with energy intake outside USDA recommendations (p < 0.05). Porphyromonas (OR = 0.51, 95% CI 0.26-0.89, p = 0.03) and Actinomyces (OR = 0.72, 95% CI 0.48-1.03, p = 0.08) were inversely associated with cachexia, although the association for Actinomyces did not reach statistical significance. Stratified analyses revealed a stronger inverse association between Porphyromonas and cachexia onset in males, patients with rectal or stage III tumors, those receiving neoadjuvant treatment, physically inactive individuals, and those consuming low fiber. However, these associations did not reach statistical significance (0.05 ≤ p < 0.10).

CONCLUSION: Higher gut microbial alpha-diversity and lower relative abundances of the genera Porphyromonas and Actinomyces in pre-surgery stool samples were associated with onset of cachexia in CRC patients six months post-surgery. This is the first study to explore a link between the gut microbiome and cachexia in CRC patients, providing novel insights into the biology of cachexia and potential clinical interventions.},
}

@article {pmid40906312,
year = {2025},
author = {Arjmand, B and Badamchizadeh, S and Mehran, P and Sarvari, M and Alavi-Moghadam, S and Arjmand, R and Rezaei-Tavirani, M and Janbabaei, G and Vaezi, M and Larijani, B},
title = {Gut Microbiome and its Impact on Outcomes following Hematopoietic Stem Cell Transplantation: a Comprehensive Review.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {40906312},
issn = {2629-3277},
abstract = {Hematopoietic stem cell transplantation is an important treatment for hematological malignancy and disorders, but is fraught with high risks, including graft-versus-host disease, infection, and relapse. Recent evidence now identifies that the microbiome plays a significant role in influencing transplant outcomes, in which microbial dysbiosis-defined by reduced diversity and pathogen overgrowth-is linked to greater complications and death. Microbiome manipulation with approaches including beneficial microbial species, fiber, fecal transplants, and diet has the potential to mitigate these risks. Experiments show that the restoration of beneficial microbes can restore immunity, reduce graft-versus-host disease severity, and reduce infection. Some challenges remain, including standardization of protocols, long-term efficacy, and safety in immunocompromised recipients. Future research will be focused on mechanisms, trials, and new technology for microbiome-based therapy, with the ultimate goal of improving survival and quality of life for transplant recipients. Hereupon, this review addresses how microbiome engineering can revolutionize cancer treatment by optimizing gut microbial communities for better outcomes in hematopoietic stem cell transplantation (HSCT).},
}

@article {pmid40906193,
year = {2025},
author = {Zambella, E and Inversetti, A and Salerno, S and Müller, M and Di Simone, N},
title = {The Father's Microbiome: A Hidden Contributor to Fetal and Long-Term Child Health.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081002},
pmid = {40906193},
issn = {2079-7737},
abstract = {The microbiota refers to the entire community of microorganisms, including bacteria, viruses, fungi, archaea, and protozoa, that inhabit various anatomical sites and exert complex influences on human health and disease [...].},
}

@article {pmid40906131,
year = {2025},
author = {Yuan, J and Sun, Z and Sun, R and Wang, J and Wu, C and Liu, B and Zhao, X and Li, Q and Zhao, J and Cai, K},
title = {A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080980},
pmid = {40906131},
issn = {2079-7737},
abstract = {The gut microbiota of macaques, highly homologous to humans in biological characteristics and metabolic functions, serves as an ideal model for studying the mechanisms of human intestinal diseases and therapeutic approaches. A comprehensive characterization of the macaque gut microbiota provides unique insights into human health and disease. This study employs metagenomic sequencing to assess the gut microbiota of wild M. mulatta brevicaudus across various ages, sexes, and physiological states. The results revealed that the dominant bacterial species in various age groups included Segatella copri and Bifidobacterium adolescentis. The predominant bacterial species in various sexes included Alistipes senegalensis and Parabacteroides (specifically Parabacteroides merdae, Parabacteroides johnsonii, and Parabacteroides sp. CT06). The dominant species during lactation and non-lactation periods were identified as Alistipes indistinctus and Capnocytophaga haemolytica. Functional analysis revealed significant enrichment in pathways such as global and overview maps, carbohydrate metabolism and amino acid metabolism. This study enhances our understanding of how age, sex, and physiological states shape the gut microbiota in M. mulatta brevicaudus, offering a foundation for future research on (1) host-microbiome interactions in primate evolution, and (2) translational applications in human health, such as microbiome-based therapies for metabolic or immune-related disorders.},
}

@article {pmid40906125,
year = {2025},
author = {Basit, A and Haq, IU and Hyder, M and Humza, M and Younas, M and Akhtar, MR and Ghafar, MA and Liu, TX and Hou, Y},
title = {Microbial Symbiosis in Lepidoptera: Analyzing the Gut Microbiota for Sustainable Pest Management.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080937},
pmid = {40906125},
issn = {2079-7737},
support = {National Natural Science Foundation of China (U22A20489; 32361143791).//National Natural Science Foundation of China (U22A20489; 32361143791)./ ; },
abstract = {Recent advances in microbiome studies have deepened our understanding of endosymbionts and gut-associated microbiota in host biology. Of those, lepidopteran systems in particular harbor a complex and diverse microbiome with various microbial taxa that are stable and transmitted between larval and adult stages, and others that are transient and context-dependent. We highlight key microorganisms-including Bacillus, Lactobacillus, Escherichia coli, Pseudomonas, Rhizobium, Fusarium, Aspergillus, Saccharomyces, Bifidobacterium, and Wolbachia-that play critical roles in microbial ecology, biotechnology, and microbiome studies. The fitness implications of these microbial communities can be variable; some microbes improve host performance, while others neither positively nor negatively impact host fitness, or their impact is undetectable. This review examines the central position played by the gut microbiota in interactions of insects with plants, highlighting the functions of the microbiota in the manipulation of the behavior of herbivorous pests, modulating plant physiology, and regulating higher trophic levels in natural food webs. It also bridges microbiome ecology and applied pest management, emphasizing S. frugiperda as a model for symbiont-based intervention. As gut microbiota are central to the life history of herbivorous pests, we consider how these interactions can be exploited to drive the development of new, environmentally sound biocontrol strategies. Novel biotechnological strategies, including symbiont-based RNA interference (RNAi) and paratransgenesis, represent promising but still immature technologies with major obstacles to overcome in their practical application. However, microbiota-mediated pest control is an attractive strategy to move towards sustainable agriculture. Significantly, the gut microbiota of S. frugiperda is essential for S. frugiperda to adapt to a wide spectrum of host plants and different ecological niches. Studies have revealed that the microbiome of S. frugiperda has a close positive relationship with the fitness and susceptibility to entomopathogenic fungi; therefore, targeting the S. frugiperda microbiome may have good potential for innovative biocontrol strategies in the future.},
}

@article {pmid40906076,
year = {2025},
author = {Zeng, Y and Shen, J and He, X and Liu, F and Wang, Y and Wang, Y and Qiao, Y and Pei, P and Wang, S},
title = {Gut Microbiota Dysbiosis Remodels the Lysine Acetylome of the Mouse Cecum in Early Life.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080917},
pmid = {40906076},
issn = {2079-7737},
support = {7242014//Beijing Natural Science Foundation Grants/ ; BMR2021-3//Public service development and reform pilot project of Beijing Medical Research Institute/ ; DFL20221102//Beijing Hospitals Authority's Ascent Plan/ ; },
abstract = {The interaction between epigenetic mechanisms and the gut microbiome is potentially crucial for the development and maintenance of intestinal health. Lysine acetylation, an important post-translational modification, plays a complex and critical role in the epigenetic regulation of the host by the gut microbiota. However, there are currently no reports on how gut microbiota dysbiosis affects host physiology in early life through global lysine acetylation. In this study, we constructed a mouse model of gut microbiota dysbiosis using antibiotic cocktail therapy (ABX). Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the cecum, we analyzed the cecal lysine acetylome and proteome. As a result, we profiled the lysine acetylation landscape of the cecum and identified a total of 16,579 acetylation sites from 5218 proteins. Differentially acetylated proteins (DAPs) are involved in various metabolic pathways, including the citrate cycle (TCA cycle), butanoate metabolism, pyruvate metabolism, glycolysis/gluconeogenesis, and fatty acid biosynthesis. Moreover, both glycolysis and gluconeogenesis are significantly enriched in acetylation and protein modifications. This study aimed to provide valuable insights into the epigenetic molecular mechanisms associated with host protein acetylation as influenced by early-life gut microbiota disturbances. It reveals potential therapeutic targets for metabolic disorders linked to gut microbiota dysbiosis, thereby establishing a theoretical foundation for the clinical prevention and treatment of diseases arising from such dysbiosis.},
}

@article {pmid40905926,
year = {2025},
author = {Fyolek, JP and Mahdavinia, M and Jiang, J and Bilaver, LA and Fox, S and Nimmagadda, SR and Newmark, PJ and Sharma, H and Assa'ad, A and Seed, PC and Gupta, RS and Warren, CM},
title = {Distinct skin microbiome signatures in Black and White children with food allergy and asthma.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {9},
pages = {e70197},
doi = {10.1111/pai.70197},
pmid = {40905926},
issn = {1399-3038},
support = {/NH/NIH HHS/United States ; },
}

@article {pmid40905862,
year = {2025},
author = {Wang, T and Lin, S and Ji, Y and Puqiong, C and Gao, J and Li, S},
title = {Prognostic impact of Fusobacterium nucleatum on survival in colorectal cancer: A systematic review and meta-analysis.},
journal = {Journal of cancer research and therapeutics},
volume = {21},
number = {4},
pages = {796-803},
doi = {10.4103/jcrt.jcrt_38_24},
pmid = {40905862},
issn = {1998-4138},
mesh = {Humans ; *Colorectal Neoplasms/mortality/microbiology/pathology ; *Fusobacterium nucleatum/isolation & purification ; Prognosis ; *Fusobacterium Infections/microbiology/complications/mortality ; Neoplasm Staging ; Survival Rate ; },
abstract = {Recent studies have demonstrated a significant correlation between Fusobacterium nucleatum (F. nucleatum) and colorectal cancer. However, the prognostic significance of this microorganism in patients with colorectal cancer remains unclear. This meta-analysis aimed to evaluate the impact of F. nucleatum on the overall survival of patients with colorectal cancer. A thorough literature search of PubMed, Embase, and Cochrane Library databases was conducted until December 2023. The hazard ratio (HR) with the corresponding 95% confidence interval (CI) was analyzed using Review Manager 5.4 software for survival outcomes, including the overall survival (OS). A total of 13 studies, covering 4475 samples with colorectal cancer, were selected based on specified inclusion and exclusion criteria. In the univariate and multivariate analyses, patients with positive or high abundance of Fusobacterium in the cancer tissues displayed poorer OS (univariate HR = 1.28, 95% CI: 1.08-1.53, P = 0.006; multivariate HR = 1.61, 95% CI: 1.37-1.88, P < 0.0001) than those with negative/low bacteria levels. Subgroup analysis revealed that Fusobacterium in cancer tissues was associated with tumor stage and differentiation. Patients with stage III and IV, T3 and T4, or poorly differentiated tumors had a higher abundance of Fusobacterium in cancer tissues than those with stage I and II, T1 and T2, or well-to-moderately differentiated tumors (P < 0.05). No statistically significant difference in lymph node metastasis was observed. These findings suggest that the Fusobacterium microbiome may play a significant role in predicting the survival outcomes in patients with colorectal cancer.},
}

Humans
*Colorectal Neoplasms/mortality/microbiology/pathology
*Fusobacterium nucleatum/isolation & purification
Prognosis
*Fusobacterium Infections/microbiology/complications/mortality
Neoplasm Staging
Survival Rate

@article {pmid40905523,
year = {2025},
author = {Hong Lee, AC and Kahaly, GJ},
title = {UNRAVELLING THE PATHOGENIC MECHANISMS IN GRAVES' ORBITOPATHY.},
journal = {European thyroid journal},
volume = {},
number = {},
pages = {},
doi = {10.1530/ETJ-25-0200},
pmid = {40905523},
issn = {2235-0802},
abstract = {Graves' orbitopathy (GO) is characterized by orbital inflammatory infiltration, expansion of orbital tissues due to de novo adipogenesis and over-production of hydrophilic glycosaminoglycans, as well as myofibroblastic differentiation resulting in tissue fibrosis. Thyrotropin receptor antibody (TSH-R-Ab) is the major stimulus, which activates Thyrotropin receptor (TSH-R) / insulin-like growth factor-1 receptor (IGF-1R) and its downstream signalling in orbital fibroblasts (OF). Clinical evaluation of TSH-R-Ab, the specific biomarker of Graves' disease (GD) and the associated orbitopathy, provides important clinical information concerning diagnosis, disease monitoring and prognosis of GO. TSH-R/IGF-1R crosstalk represents the principal mechanism of activation of OF, the key effector cells in GO. T cell and monocytes/macrophages predominate in the inflammatory infiltrates and B-T cell co-stimulation results in mutual activation. Mast cell-derived products also activate OF. In the presence of various pro-inflammatory molecules, activated OF and lymphocytes perpetuate orbital inflammation and mediate tissue remodelling. Enhanced oxidative stress drives various pathological processes in GO and many antioxidant agents have shown inhibitory effects on OF. Highly differential gene and protein expression exists between GO and normal subjects, as well as between active/severe and inactive/mild GO, providing important insights into the disease mechanisms. The lack of confirmed genetic susceptibility to GO development suggests that epigenetic mechanisms (e.g. DNA methylation, microRNAs) may play a role in regulating gene and protein expression, and hence disease phenotypes. Gut microbiome differs significantly between GO patients and healthy individuals. Modifying gut microbiota in GO animal models improves GO. Emerging evidence indicates that hypercholesterolemia is associated with increased risk of developing GO, while statin use is a protective factor.},
}

@article {pmid40905407,
year = {2025},
author = {Figuerola, B and Linares, C and Aparicio-Estalella, C and López-Sendino, P and Garrabou, J and Del Campo, J},
title = {Microbiome Composition in a Common Mediterranean Bryozoan Following an Unprecedented Marine Heatwave.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70185},
doi = {10.1111/1758-2229.70185},
pmid = {40905407},
issn = {1758-2229},
support = {RYC2022-036268-I//Ramón y Cajal/ ; 2019 BP 00183//Beatriu de Pinós/ ; 801370//Catalan Government and the European Union's Horizon 2020/ ; PID2021-125323OA-I00//MedCalRes/ ; CNS2024-154224//HOLOCHANGE/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; 2021 SGR 01073//Generalitat de Catalunya/ ; //ICREA/ ; //Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {*Bryozoa/microbiology ; Animals ; *Microbiota ; Hot Temperature ; Global Warming ; *Bacteria/classification/genetics/isolation & purification ; Mediterranean Sea ; Seawater/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Marine heatwaves are intensifying due to global warming and increasingly drive mass mortality events in shallow benthic ecosystems. Marine invertebrates host diverse microbial communities that contribute to their health and resilience, yet microbiome responses under thermal stress remain poorly characterised across most taxa. Here, we characterise the microbiome composition in colonies of the common Mediterranean bryozoan Myriapora truncata at two depths (13 and 17 m) following the extreme 2022 marine heatwave. Despite no visible necrosis, microbial communities at both depths exhibited shifts indicative of thermal stress, including the reduced presence of potential core microbial members. Colonies from the shallower, warmer depth showed higher alpha diversity and reduced abundance of key functional genera compared to deeper colonies, suggesting early dysbiosis. These results highlight that M. truncata-though visually unaffected-undergoes sublethal microbiome alterations under thermal stress. This study provides the first characterisation of a bryozoan microbiome after a marine heatwave and highlights the potential of host-associated microbial communities as early bioindicators of invertebrate stress in a warming ocean.},
}

*Bryozoa/microbiology
Animals
*Microbiota
Hot Temperature
Global Warming
*Bacteria/classification/genetics/isolation & purification
Mediterranean Sea
Seawater/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid40905340,
year = {2025},
author = {Carolyn, M and Strysko, J and Bayani, O and Moorad, B and Ntlhako, N and Nwako, N and Hu, W and Tanes, C and Moustafa, AM and Jones, SM and Nakstad, B and Gezmu, AM and Arscott-Mills, T and Goldfarb, DM and Steenhoff, AP and Richard-Greenblatt, M and Machiya, T and Thela, T and Mokomane, M and Paganotti, GM and Vurayai, M and Zalot, M and Boustany, M and Planet, PJ and Coffin, S and Bittinger, K},
title = {Effect of maternal HIV status on the early neonatal microbiome.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piaf076},
pmid = {40905340},
issn = {2048-7207},
abstract = {Microbiome disruption is a proposed mechanism for the observed differences in child health outcomes by maternal HIV status, but the early neonatal microbiome of HIV-exposed (HE) newborns is not well studied. We used 16S ribosomal ribonucleic acid sequencing to analyze the microbiome composition of nasal, skin, and rectal samples collected ≤72 hours after birth from 57 hospitalized neonates in Botswana, 33% of whom were HE. Beta diversity differed by anatomic compartment (p=.001) and days since birth; however, interindividual differences were greater than those by anatomic site (p=.001). There were not significant differences by maternal HIV status. When timing of maternal HIV diagnosis was accounted for, however, we noted statistically significant differences in beta diversity for nasal and skin swabs. Microbial composition of samples from neonates with mothers diagnosed with HIV prior to pregnancy were more similar to samples from HIV-unexposed than HE neonates with mothers diagnosed with HIV during this pregnancy (p=.03 and p<.01 in skin and nasal respectively) suggesting that microbiome variations mediated by HIV exposure might only emerge later in infancy. In the entire cohort, we examined differences in relative taxa abundance of neonatal pathogens and other species of clinical interest. We noted differences by anatomic compartment, for example increased Klebsiella pneumoniae in rectal samples and increased Acinetobacter baumannii in nasal samples, whereas other pathogens expected to differ by body site did not, for example Enterococcus faecium and Streptococcus agalactiae, highlighting that in the early neonatal microbiome exposures may have a significant impact on microbiome development.},
}

@article {pmid40905153,
year = {2025},
author = {Haferkamp, S and Schilling, B and Berking, C and Drexler, K and Gesierich, A and Tomsitz, D and Erdmann, M and Jakob, L and Geissler, EK and Zeman, F and Heinzerling, L},
title = {Breaking primary checkpoint inhibitor resistance with intermittent alkylating chemotherapy in patients with metastatic melanoma - Results of a multicenter phase II study.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf350},
pmid = {40905153},
issn = {1365-2133},
abstract = {BACKGROUND: Patients with BRAF wild type (wt) metastatic melanoma who exhibit primary resistance to immune checkpoint inhibitors (ICI) face a poor prognosis. Chemotherapy has been shown to induce genetic mutations, modify the tumor microenvironment and microbiome, and influence immune system activity.

OBJECTIVES: This prospective multicenter phase II trial investigates whether two applications of an alkylating agent (dacarbazine/DTIC) can sensitize ICI non-responsive patients with metastatic melanoma to the same checkpoint inhibitor regime.

METHODS: The PROMIT trial (NCT04225390) enrolled patients with histologically confirmed BRAF wt metastatic melanoma who exhibited primary resistance to ICI therapy. Following radiologic evidence of primary resistance to ICI (ipilimumab plus nivolumab or pembrolizumab) upon the first staging after initiation, patients received two doses of DTIC at 850 mg/m² intravenously on days 1 and 21. Subsequently, 1 week after application of the second dose of DTIC, patients were re-challenged with the same ICI therapy to which they had previously shown progressive disease.

RESULT: In total, 53 patients were enrolled across four German skin cancer centers. Of these, 38 patients were evaluable for efficacy, having received at least one dose of ICI re-exposure. The overall objective response rate was 18.4% (95% CI 0.08-0.34), with 7 out of 38 patients achieving a partial response. The disease control rate was 36.8%. Therapy was well tolerated, with grade 3 CTCAE or higher adverse events occurring in 10.4% of patients, and no new safety signals were observed.

CONCLUSIONS: Study results indicate that short-term chemotherapy followed by ICI re-challenge can overcome primary ICI resistance in melanoma patients, supporting its potential as a new therapeutic option in clinical practice.},
}

@article {pmid40904962,
year = {2025},
author = {Asante Baadu, F and Ahsan, M and Hussain, B and Hussain, S and Malik, H and Naqvi, SS and Mustafa, Z and Zahid, M and Ahmad, RT},
title = {Microbiome Imbalance and Pediatric Type 1 Diabetes Mellitus: An Updated Systematic Review of Gut Dysbiosis Evidence.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89279},
pmid = {40904962},
issn = {2168-8184},
abstract = {Emerging evidence suggests that alterations in the gut microbiota may play a significant role in the development of type 1 diabetes mellitus (T1DM), particularly during childhood, when the immune and metabolic systems are still maturing. This systematic review aims to synthesize recent findings on the composition, diversity, and functional characteristics of gut microbiota in children with T1DM. A comprehensive literature search was conducted on PubMed, Cochrane Library, and Google Scholar for studies published between January 2019 and July 2025. Eligible studies included observational studies examining the gut microbiota in children with T1DM using validated sequencing methods. Six studies met the inclusion criteria and were analyzed for microbial composition, diversity, and associated immune and metabolic alterations. Most studies reported reduced microbial diversity and depletion of short-chain fatty acid (SCFA)-producing bacteria, such as Faecalibacterium and Roseburia, in T1DM children. An increased abundance of pro-inflammatory genera, including Bacteroides, Blautia, and Dorea, was frequently observed. Several studies have also identified elevated levels of gut permeability markers, such as zonulin and lipopolysaccharide (LPS), suggesting compromised intestinal barrier function. Notably, while some studies reported decreased abundance of Parasutterella in T1DM, one study observed its increased abundance, indicating regional or methodological variability. Gut dysbiosis, characterized by reduced diversity, loss of beneficial microbes, and increased intestinal permeability, is consistently associated with pediatric T1DM. However, the heterogeneity of specific taxa highlights the need for standardized longitudinal research. Understanding gut microbial alterations may provide novel opportunities for early intervention and disease modulation in at-risk children.},
}

@article {pmid40904740,
year = {2025},
author = {Sapthanakorn, T and Choopong, P and Sermsripong, W and Boriboonhirunsarn, C and Khamwachirapitak, C and Krasaesin, A and Sutthiboonyaphan, P and Siripaiboonpong, N and Mahanonda, R and Wiriyakijja, P and Pelekos, G and Porntaveetus, T and Srithanyarat, SS},
title = {Functional and taxonomic dysbiosis of the supragingival plaque metagenome in Behçet's disease.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2552165},
pmid = {40904740},
issn = {2000-2297},
abstract = {BACKGROUND: Behçet's Disease (BD), a complex autoinflammatory disorder, is increasingly linked to microbial dysbiosis, yet the specific microbial signatures and their functional consequences remain incompletely characterized. Elucidating these alterations is crucial for understanding BD pathogenesis.

OBJECTIVE: To identify distinct microbial community structures and functional potentials in supragingival plaque microbiomes of BD patients versus healthy controls (HC) using high-resolution shotgun metagenomic sequencing.

METHODS: Supragingival plaque from 18 BD patients and 22 HCs was subjected to shotgun metagenomics. Analyses included alpha/beta diversity, taxonomic composition, and MetaCyc pathway abundance, with statistical comparisons.

RESULTS: Despite similar age and clinical attachment levels, BD patients exhibited significantly increased alpha diversity and distinct beta diversity compared to HCs. Differential abundance analysis revealed an enrichment of anaerobic and opportunistic taxa in BD (implicating 4 phyla and 28 genera), alongside 19 significantly altered MetaCyc pathways, indicating substantial functional reprogramming within the BD oral microbiome.

CONCLUSION: This high-resolution metagenomic analysis reveals profound oral microbiome dysbiosis in Behçet's Disease, characterized by altered diversity, a distinct taxonomic signature enriched with pathobionts, and significant functional shifts. These comprehensive microbial alterations are implicated in contributing to the local and systemic inflammatory processes driving BD pathogenesis, offering potential avenues for diagnostic biomarkers and targeted therapies.},
}

@article {pmid40904642,
year = {2025},
author = {Sun, Q and Jiang, Z and Yang, L and Liu, H and Song, P and Yuan, L},
title = {Towards an Asian paradigm of inflammatory bowel disease management: A comparative review of China and Japan.},
journal = {Intractable & rare diseases research},
volume = {14},
number = {3},
pages = {192-202},
pmid = {40904642},
issn = {2186-3644},
abstract = {This systematic review compares inflammatory bowel disease (IBD) management between China and Japan across epidemiology, clinical strategies, health insurance, and social security policies. Epidemiologically, the incidence of IBD is rapidly increasing in China, contributing to a growing disease burden. In contrast, Japan has a stabilized incidence but a rising prevalence, driven by an aging patient population. Clinically, step-up therapy remains the mainstream approach in China, limited by regional and financial disparities in biologic access. In contrast, Japan, benefiting from the "Designated Intractable Diseases" program, favors early intensive therapy with a focus on mucosal healing. In the area of precision medicine, China is advancing rapidly in therapeutic drug monitoring (TDM) for anti-TNF agents. In contrast, Japan leads in AI-assisted endoscopic assessment, despite slower adoption of TDM. Japan's comprehensive insurance covers most costs of IBD; China has significantly reduced drug prices via national negotiations, and yet reimbursement rates vary regionally. China has made progress in telemedicine and standardized fecal microbiota transplantation (FMT); Japan excels in AI endoscopy and use of an elemental diet. To optimize IBD care in the Asia-Pacific, China should enhance access to advanced therapies, implement hierarchical diagnosis/ treatment, and develop multi-tiered insurance. Japan must address aging-related challenges and insurance sustainability while expanding use of TDM. Sino-Japanese collaboration in genetics, microbiome research, and AI-driven diagnostics, supported by sustained policy dialogue, is key to advancing precision IBD care and shaping a scalable "Asian model" for chronic disease management.},
}