@article {pmid40619188,
year = {2025},
author = {Hackman, NM and Hoyt-Austin, AE and Fernández, CR and Kair, LR},
title = {Recent Advancements and Best Practices in Supporting Newborn Feeding: A Narrative Review.},
journal = {Pediatric clinics of North America},
volume = {72},
number = {4},
pages = {581-595},
doi = {10.1016/j.pcl.2025.04.001},
pmid = {40619188},
issn = {1557-8240},
mesh = {Humans ; Infant, Newborn ; *Breast Feeding/methods ; *Infant Nutritional Physiological Phenomena ; *Infant Care/methods ; Practice Guidelines as Topic ; },
abstract = {Care of the newborn can be complex and very rewarding. The pediatric clinician will face the important challenge of balancing and supporting a family's feeding plan with the health care needs of the newborn and lactating parent. This narrative review focuses on several important topics and provides valuable resources and guidance in the complex care of newborn feeding. The health benefits of breastfeeding, benefits of skin to skin, guidance on unique or complex newborn feeding situations, response to newborn weight loss, vitamin supplementation, as well as consideration of the social determinants of health in the context of infant feeding are reviewed.},
}

Humans
Infant, Newborn
*Breast Feeding/methods
*Infant Nutritional Physiological Phenomena
*Infant Care/methods
Practice Guidelines as Topic

@article {pmid40619159,
year = {2025},
author = {Hou, J and Weng, A and Yang, Z and Huang, X and Chen, W and Wang, X},
title = {Unveiling the Link Between Oral Microbiome Diversity and Biological Ageing: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14172},
pmid = {40619159},
issn = {1600-051X},
abstract = {AIM: To investigate the relationship between oral microbiome diversity and biological ageing acceleration in a nationally representative U.S.

METHODS: Data from 7716 participants in NHANES (2009-2012) were analysed. Oral microbiome diversity was assessed, and biological ageing acceleration was calculated using a validated algorithm. Generalised linear models, restricted cubic splines and smooth curve fitting were applied to evaluate associations.

RESULTS: Higher α-diversity of the oral microbiome was significantly negatively correlated with biological ageing acceleration. Stratified analyses revealed that this protective effect was particularly pronounced in men and individuals with hypertension and diabetes. β-Diversity analysis showed significant differences in the association between microbial community composition and biological ageing acceleration, with immune functions potentially modulating these effects. Furthermore, key intervals of α-diversity were identified, which may serve as potential targets for future research on delaying ageing.

CONCLUSIONS: In the general U.S. population, greater oral microbiome diversity was associated with lower biological ageing acceleration, especially among men and those with hypertension and diabetes. This association was also observed in Mexican and Hispanic populations.},
}

@article {pmid40619037,
year = {2025},
author = {Karine da Rosa Dias, K and Tochetto, C and Muterle Varela, AP and Loiko, MR and Caroline Dos Santos, A and Frazzon, J and Roehe, PM and Mayer, FQ},
title = {Impact of weaning on piglet microbiota: differences in bacterial taxa and metabolic pathways associated with diarrhea.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107878},
doi = {10.1016/j.micpath.2025.107878},
pmid = {40619037},
issn = {1096-1208},
abstract = {In modern pig farming, early weaning increases pigs' vulnerability to intestinal diseases due to the immaturity of their digestive and immune systems. Post-weaning diarrhea is a common issue in Brazil, leading to weight loss and slow growth, which significantly impacts the swine industry's performance. The intestinal microbiota plays a crucial role during this phase, as it is determinant for the animals' health and productivity. This study aimed to compare the microbiota of post-weaning piglets with and without diarrhea, identifying differences in the bacterial composition and microbial metabolic pathways. The most frequent phyla in both groups were Bacillota followed by Bacteriodota and Pseudomonadota, which together accounted for nearly 90% of microbiota. However, one phylum and eight bacterial families were enriched in the control group (minimum fold change of 4.6), whereas only the Fusobacteriaceae family was enriched in diarrhea group (fold change of 6.5). Moreover, 16 genera were enriched in the control group, while 12 were enriched in the diarrhea group. These findings indicate distinct microbiota compositions between the groups, suggesting an association with dysbiosis. Variations in metabolic pathways were also observed. In the diarrhea group, six pathways were enriched (fold changes of 8.12 to 263.23), most of which were associated with pathogenic and inflammatory processes. In addition, an increase in pathways linked to bacterial metabolism suggested heightened microbial activity, potentially exacerbating diarrhea. In contrast, seven metabolic pathways were enriched in the control group, many of which are essential for immune system development and strengthening, supporting healthy growth. These results highlight key differences in the microbiota and metabolic activity of piglets with and without diarrhea, providing insights that may aid in developing strategies to promote intestinal health and improve post-weaning performance.},
}

@article {pmid40619005,
year = {2025},
author = {Hullar, MAJ and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW},
title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.026},
pmid = {40619005},
issn = {1938-3207},
abstract = {BACKGROUND: Dietary patterns characterized by low-glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.

OBJECTIVE: Evaluate the effects of a low glycemic load (LGL) versus a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.

METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n=69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.

RESULTS: Overall community structure measured by alpha and beta diversity were not significantly different across the diets although diet did significantly increase the abundance of 13 out of 161 genera (padj<0.05) and 5 species in the LGL and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (β=-1.15, SE=0.24 with 95% CI (-1.63, -0.67); padj=0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (β =0.20, SE=0.05 with 95% CI (0.09, 0.30); padj=0.03); was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, p<0.001). CAZymes enriched in the HGL diet reflected dietary additives while CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between HOMA IR and the Coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (padj=0.035) that was positive in the HGL diet (β=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (β =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).

CONCLUSION: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}

@article {pmid40618920,
year = {2025},
author = {Kongsintaweesuk, S and Tunbenjasiri, K and Pongking, T and Roytrakul, S and Charoenlappanit, S and Anutrakulchai, S and Pairojkul, C and Intuyod, K and Tanasuka, P and Blair, D and Pinlaor, S and Pinlaor, P},
title = {Microcystin-LR exacerbates chronic kidney disease in rats: Insights into gut microbiome and host proteome dysregulation.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123840},
doi = {10.1016/j.lfs.2025.123840},
pmid = {40618920},
issn = {1879-0631},
abstract = {AIMS: This study aimed to investigate the effects of microcystin-leucine arginine (MC-LR), an environmental nephrotoxin, on the gut-kidney axis in chronic kidney disease (CKD), focusing on interactions between the gut microbiome and host proteome.

MATERIALS AND METHODS: Male Sprague-Dawley rats were administered adenine (200 mg/kg/day) for 10 days to induce kidney injury, followed by MC-LR (10 μg/mL/kg, i.p., every other day for 4 weeks). Renal function (Blood urea nitrogen (BUN), Serum creatinine (SCr), and urine albumin to creatinine ratio (uACR)) and kidney pathology (EGTI histology scores and picrosirius-red staining) were assessed. Expression of kidney injury (KIM-1), fibrosis (CTGF), inflammation (HMGB1 and CD3), oxidative stress (H2AX) markers were evaluated by immunohistochemical staining. Gut microbiota was analyzed by 16S rRNA sequencing, and fecal proteomics by LC-MS/MS.

KEY FINDINGS: MC-LR markedly exacerbated adenine-induced kidney injury, leading to impair kidney function (elevated BUN, Cr, and uACR levels) and worsen kidney histopathology (higher EGTI histology scores and prominent fibrosis). Elevated expression levels of KIM1, HMBG1, CTGF, H2AX and CD3 were observed following MC-LR exposure. Notably, pro-inflammatory bacterial families (Enterococcaceae, Enterobacteriaceae) were elevated, while beneficial taxa (Bifidobacteriaceae, Muribaculaceae) decreased in the combination group. Proteomic analysis revealed upregulation of inflammatory markers (TXNIP, Itgb3bp), which correlated with Enterococcaceae abundance. Bifidobacteriaceae negatively correlated with kidney injury markers.

SIGNIFICANCE: Our study reveals that MC-LR exacerbates chronic kidney disease progression by disrupting the gut-kidney axis. We highlight gut barrier integrity and inflammation as crucial therapeutic targets, offering novel insights and intervention strategies for CKD management, particularly in beyond early stages.},
}

@article {pmid40618877,
year = {2025},
author = {Luo, Y and Tan, C and Yang, J and Zhang, G and Wu, J},
title = {Maternal exposure to tris (2-chloroethyl) phosphate during pregnancy and suckling period alters gut microbiota and SCFAs metabolism in offspring of rats.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126777},
doi = {10.1016/j.envpol.2025.126777},
pmid = {40618877},
issn = {1873-6424},
abstract = {Tris(2-chloroethyl) phosphate (TCEP), one of the most widely used organophosphate flame retardants, is frequently detected in environmental and biological samples. However, its toxic effects on the offspring remain unknown. To explore the health risks posed by TCEP in susceptible populations, we investigated the intergenerational transmission of TCEP, gut microbiome, and disruptive effects of intestinal metabolites in the offspring. Different doses of TCEP were administered orally to female Sprague-Dawley (SD) rats throughout pregnancy or during both pregnancy and lactation periods. Concentrations of TCEP and its metabolite, BCEP, composition of the gut microbiota, and fecal concentrations of short-chain fatty acids were measured. The concentration of TCEP in the placenta of rats in the high-dose group was significantly higher than that in the control group, and BCEP was also present. Serum and fecal samples from immature offspring contained TCEP; however, no BCEP was detected in serum. Exposure to TCEP altered the intestinal microbiota of both the maternal rats and their offspring. The relative abundance of Coelenterata was significantly increased in the immature offspring. Exposure to TCEP altered the concentration of SCFAs in the feces of the rats and their offspring. Lower concentrations of acetic, propionic, and butyric acids were observed in the feces of immature offspring. Holdemanella had a significant mediating effect between TCEP exposure and intestinal concentrations of acetic and propionic acids. Maternal exposure to TCEP affects the gut microbiota balance and metabolism of offspring, suggesting the presence of a long-term risk associated with metabolic disease.},
}

@article {pmid40618613,
year = {2025},
author = {Nie, S and Shen, C and Qu, S and Chen, B and Liu, S and Ge, Y},
title = {Predicting the impact of climate warming on soil quality using bacteria and machine learning.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126473},
doi = {10.1016/j.jenvman.2025.126473},
pmid = {40618613},
issn = {1095-8630},
abstract = {In the context of global warming, a substantial portion of global soil is in a state of degradation, which poses a significant threat to biodiversity and food production worldwide. Moreover, monitoring soil quality typically requires measuring numerous physical, chemical, and biological indicators, resulting in high costs. In this study, 286 soil samples were obtained from the climate-sensitive Tibetan Plateau and subjected to 16S rRNA amplicon sequencing to reveal the relationships between soil quality, soil bacteria, and climate warming. The results indicated that climate-sensitive bacteria could effectively predict soil quality indices through machine learning (R[2] > 0.76). This suggests that 16S rRNA sequencing can replace numerous soil indicators, providing comprehensive information on soil quality and reducing the costs associated with soil quality monitoring. Additionally, model predictions demonstrated a slight increase in soil quality when only the average annual temperature increased by 1.5 °C. However, when other climatic factors (precipitation and temperature during specific periods) also changed (future climate scenarios for 2021-2040 and 2080-2100), which is more realistic than only increasing the average annual temperature, soil quality declined and the greater the increase in temperature, the more severe the decline in soil quality. These findings provide valuable insights for soil management in the face of increasingly severe climate warming conditions. In summary, our research offers new perspectives for soil quality monitoring from a microbiome standpoint and indicates that future climate warming could pose a threat to soil quality.},
}

@article {pmid40618567,
year = {2025},
author = {Schäfer, L and Grundmann, SM and Hepp, V and Herrero-Encinas, J and Rühl, M and Most, E and Ringseis, R and Eder, K},
title = {Influence of Pleurotus sapidus fruiting bodies on the performance, cecal microbiome, and gene expression in the liver and breast muscle of broilers.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105517},
doi = {10.1016/j.psj.2025.105517},
pmid = {40618567},
issn = {1525-3171},
abstract = {Mushrooms, the fruiting bodies of edible fungi, are widely used as food for humans. However, their potential, as well as that of fungal mycelia, as feed components for poultry is less acknowledged. Recent studies have shown that feeding the vegetative mycelium of Pleurotus sapidus does not affect growth performance or nutrient digestibility and causes only minimal changes in the cecal microbiota structure, liver transcriptome, and plasma metabolome of broilers. The present study aimed to comprehensively investigate the effects of feeding the fruiting bodies of P. sapidus on performance metrics, ileal nutrient digestibility, cecal microbiota composition, cecal integrity, liver transcriptome, and the expression of genes involved in protein turnover in breast muscle of broilers. A total of 72 male, 1-day-old Cobb 500 broilers were randomly assigned to three groups and fed three distinct diets containing either 0 g (PSA-F0), 25 g (PSA-F25), or 50 g (PSA-F50) of freeze-dried P. sapidus fruiting bodies per kg diet in a 35-day, three-phase feeding regimen. Final body weights and weight gain during the finisher and the whole period were significantly lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.05). Feed intake during the finisher and the whole period tended to be lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.1). Average daily apparently digested amounts of most indispensable amino acids were lower in group PSA-F50 than in group PSA-F0 (P < 0.05). Cecal microbial α-diversity indicators (Chao1 and Richness) were significantly higher in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), whereas β-diversity indicators were similar between groups. Taxonomic analysis showed a higher abundance of the class Bacilli and the species unknown_Erysipelatoclostridium and a lower abundance of the class Clostridia in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). Concentrations of total and individual short-chain fatty acids, including acetic acid and propionic acid, in the cecal digesta were lower in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). A total of 66 differentially expressed transcripts were identified in the liver between PSA-F50 and PSA-F0 groups based on filter criteria (FC > 1.3 or FC < -1.3, P < 0.05). The mRNA levels of genes involved in critical pathways such as protein synthesis and degradation-including the mammalian target of rapamycin pathway, myogenesis, the ubiquitin-proteasome system, autophagy-lysosomal pathway, and GCN2/eIF2α pathway-did not vary across the groups. Plasma lipopolysaccharide concentration was similar across all groups. The mRNA levels of CLDN3, MUC2, and MUC5AC were elevated in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), while mRNA levels of CLDN5, OCLN, MUC13, and several pro-inflammatory genes in cecal mucosa remained unchanged across groups. The observed impairment in growth performance suggests that P. sapidus fruiting bodies cannot be recommended as dietary components for broilers at the tested doses. Considering the higher β-glucan content of fruiting bodies compared to vegetative mycelia, the negative effects observed on broiler performance may be associated with their β-glucan content.},
}

@article {pmid40618523,
year = {2025},
author = {Yin, YL and Xu, YX and Wang, MT and Yang, DZ and Wang, XY and Zhou, XK and Huang, MM and Yang, S and Fei, H},
title = {Integrative analysis of microbiome and metabolome reveals the effect of deoxynivalenol on growth performance, liver and intestinal health of largemouth bass (Micropterus salmoides).},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139148},
doi = {10.1016/j.jhazmat.2025.139148},
pmid = {40618523},
issn = {1873-3336},
abstract = {This study explored the toxic effects of deoxynivalenol (DON) intake at low (100 µg·Kg[-1], LD group) and high doses (300 µg·Kg[-1], HD group) on largemouth bass (Micropterus salmoides). After a 56-day feeding trial, the HD group exhibited significantly reduced growth performance and weakened antioxidant capacity, along with elevated activities of enzymes related to metabolic dysregulation. Histopathological analysis showed an increase in hepatic cell vacuoles, as well as a shortened intestinal villi in both LD and HD groups. Notably, high-dose DON intake markedly down-regulated the expression of intestinal epithelial tight junction-related genes and proteins. Microbiome analysis indicated a significant increase in the Delftia and Acinetobacteria relative abundance, accompanied by diminished in Mycoplasma abundance in the HD group. Metabolomic profiling demonstrated that the dysregulated metabolites were mainly associated with the lysine biosynthesis pathway. Integrative multi-omics analysis revealed that pyridoxamine and diferuloylputrescine served as key biomarkers associated with Acinetobacteria. Collectively, we confirmed that high-dose DON intake induces hepatointestinal damage, thereby impairing the growth performance of largemouth bass. Our findings also further highlighted the link between DON-induced gut microbiota alterations and metabolic disorders, offering new intervention targets for alleviating DON toxicity.},
}

@article {pmid40618487,
year = {2025},
author = {Schober, JM and Wilson, N and Seyoum, MM and Lyte, JM and Bergman, MM and Oluwagbenga, EM and Fraley, GS},
title = {Effects of semi-open water and non-water enrichment on welfare, production, behavior, and microbial exposure of grow-out Pekin ducks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105477},
doi = {10.1016/j.psj.2025.105477},
pmid = {40618487},
issn = {1525-3171},
abstract = {Environmental enrichment plays an important role in the welfare, behavior, and health of commercially raised Pekin ducks. We assessed the effects of three enrichment treatments and a control: Nipple line (CON), whiffle ball (EED), preening cup (PC), and Pekino (PEK) on duck welfare, behavior and bacterial exposure. 525 grow-out Pekin ducks were housed in 4 pens/4 rooms with one of the four enrichment types (N = 4 pens/treatment). Body weights and body condition scores of 10 ducks/pen and FCR, ammonia level, and litter moisture % were recorded weekly. On 16 and 44 days of age, 3 ducks/pen were euthanized and their organs were weighed and whole brains collected. Behavior data were collected using scan sampling with video being recorded for 72 continuous hours for 3 weeks after enrichment placement. Weekly samples were also collected for viable bacterial counts, and 16S rRNA gene sequencing at baseline and 6 h after baseliner. Body morphometrics, FCR, ammonia levels, litter moisture % and viable bacteria were analyzed by 2-way ANOVA with repeated measures. Body condition scores were analyzed with PROC LOGISTIC (SAS 9.4). GLIMMIX procedure (SAS 9.4) was used to analyze behavior. Bacterial communities were characterized using 16S rRNA gene sequencing, and functional potential was predicted using PICRUSt2. PEK and PC ducks were largest in weight (p < 0.0001) and better nostril scores (p = 0.0005) but had dirtier feathers (p < 0.0001), worse litter conditions (p < 0.0001) and more viable bacteria in their water sources (p < 0.0001), while the PC and EED ducks had worse feather quality (p = 0.0021). Alpha and beta diversity metrics revealed that microbiota composition was significantly (p < 0.05) dependent on environmental enrichment type. Likewise, functional pathway analyses revealed distinct (p < 0.05) metabolic capacities, including aerobic respiration and amino acid biosynthesis, between microbiotas of each respective environmental enrichment niche. Our study suggests that semi-open water sources and EEDs may lead to an increase in feather pecking and a decrease in feather quality with a low number of ducks per enrichment as well as an increase in bacteria load and litter moisture.},
}

@article {pmid40618377,
year = {2025},
author = {Le, TT and Hoang, TN and Do, DH and Nguyen, XH and Huynh, C and Viet, HD and Dat, VQ and Zengler, K and Gilbert, JA and Avedissian, SN and Tran, TM and Le, J},
title = {Current state of microbiota clinical applications in neonatal and pediatric bacterial infections.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2529400},
doi = {10.1080/19490976.2025.2529400},
pmid = {40618377},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; Child ; *Bacterial Infections/microbiology/therapy ; Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Infant ; Bacteria/classification/isolation & purification/genetics ; Child, Preschool ; },
abstract = {The microbiota plays a crucial role in pediatric health by shaping immune development and influencing infection susceptibility. In infants and children, an immature microbiota may compromise immune defense, increasing the risk of bacterial infections. This review evaluates clinical trials on the microbiota's role in neonatal and pediatric bacterial infections, including sepsis, infections in pediatric cancer patients, and Clostridioides difficile-associated dysbiosis. We summarized original research articles published from 2000 to May 2024 on the microbiota and bacterial infections in neonates and children. A balanced microbiota is essential for infection prevention, particularly in premature infants and immunocompromised children. Studies of microbiome signatures in the gut, oral cavity, and nasopharynx have highlighted how microbiota composition influences infection risk, treatment response, and adverse effects from antibiotics and chemotherapy. Disruptions from antibiotic exposure, chemotherapy, and hematopoietic stem cell transplantation frequently lead to dysbiosis, characterized by depletion of commensal bacteria and overgrowth of pathobionts, including antibiotic-resistant strains such as C. difficile. Conversely, microbiota-restorative interventions, such as probiotics and fecal microbiota transplantation, show promise in reducing bacterial infections by enhancing microbial resilience. The microbiota plays a critical role in predicting and potentially treating bacterial infections in children. While antibiotics remain essential, their widespread use has significant consequences for microbiota health. Striking a balance between effective infection control and microbiota preservation is crucial, particularly in vulnerable pediatric populations. Implementing judicious antibiotic use and exploring microbiota-based therapies may mitigate long-term microbiota disruptions, ultimately improving infection outcomes and overall pediatric health.},
}

Humans
Infant, Newborn
Child
*Bacterial Infections/microbiology/therapy
Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome
Anti-Bacterial Agents/therapeutic use
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Infant
Bacteria/classification/isolation & purification/genetics
Child, Preschool

@article {pmid40618373,
year = {2025},
author = {Li, L and Yang, Z and Yi, Y and Song, Y and Zhang, W},
title = {Gut microbiota and radiation-induced injury: mechanistic insights and microbial therapies.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2528429},
doi = {10.1080/19490976.2025.2528429},
pmid = {40618373},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/radiation effects ; *Radiation Injuries/therapy/microbiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Signal Transduction ; Oxidative Stress ; Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Prebiotics ; },
abstract = {Radiotherapy represents a crucial therapeutic modality in cancer treatment, yet its efficacy is frequently limited by radiation-induced toxicity. Growing evidence indicates that gut microbiota and their metabolites serve as key regulators of both radioprotective and radiosensitizing effects. This review systematically examines three fundamental regulatory mechanisms through which gut microbiota and its metabolites mitigate radiation-induced injury: (1) modulation of intestinal epithelial cell regeneration and tumor cell apoptosis via Wnt/β-catenin and PI3K/AKT/mTOR pathways; (2) immunomodulation via Toll-like receptor activation and NF-κB signaling; (3) oxidative stress management via Nrf2 signaling. We also evaluate various microbiota-targeted interventions, ranging from probiotics and prebiotics to fecal microbiota transplantation and emerging engineered microbial therapies, highlighting their potential in clinical radiotherapy. Finally, we emphasize current limitations and future research directions, underscoring the need to overcome existing challenges in microbiome analysis and therapeutic durability to fully realize the potential of precision radio-microbiome medicine, which may provide valuable references for developing personalized radiotherapy strategies based on gut microbiota and their metabolites.},
}

Humans
*Gastrointestinal Microbiome/physiology/radiation effects
*Radiation Injuries/therapy/microbiology
Animals
Fecal Microbiota Transplantation
Probiotics
Signal Transduction
Oxidative Stress
Neoplasms/radiotherapy
Radiotherapy/adverse effects
Prebiotics

@article {pmid40618372,
year = {2025},
author = {Healy, DB and Wang, S and Patangia, D and Grimaud, G and Ross, RP and Stanton, C and Dempsey, EM},
title = {Late-onset sepsis treatment in very preterm infants alters longitudinal microbiome trajectory with lower abundance of Bifidobacterium despite probiotic supplementation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2523808},
doi = {10.1080/19490976.2025.2523808},
pmid = {40618372},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Longitudinal Studies ; Infant, Newborn ; Male ; *Sepsis/microbiology/drug therapy/therapy ; Female ; *Bifidobacterium/isolation & purification/genetics/growth & development ; Feces/microbiology ; Anti-Bacterial Agents/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infant, Premature ; Bacteria/classification/genetics/isolation & purification ; Dietary Supplements ; Infant ; },
abstract = {INTRODUCTION: Taxonomic instability within the dynamic gut microbiome of very preterm infants can be associated with various adverse outcomes. This longitudinal study was designed to follow the trajectory of microbiome composition and abundance in a cohort of probiotic supplemented very preterm infants with and without sepsis.

METHODS: Stool samples (n = 180) from probiotic-supplemented participants with culture-positive sepsis (n = 8) and matched healthy controls (n = 10) were analyzed using 16S rRNA sequencing. Calculation of total copy number per gram (TCN/g) by DNA spiking provided estimates of total microbial load.

RESULTS: TCN/g was significantly different between infants with and without sepsis, the latter having more rapid increase and overall higher TCN/g. In adjusted analysis, sepsis was associated with a significant abundance of Escherichia-Shigella (p = 0.02) and Veillonella (p = 0.01). Microbial load and composition appeared to fluctuate following antibiotic administration. Analysis of pre-sepsis samples showed a non-significant trend toward lower Bifidobacterium abundance and higher Escherichia-Shigella abundance in infants with subsequent sepsis. Antibiotic administration was independently associated with significantly lower (on average 250-fold lower) Bifidobacterium (p = 0.005) abundance, which remained significant after adjustment for confounders.

CONCLUSIONS: Estimation of absolute abundance reveals fluctuations and blooms in key genera within the gut microbiome of very preterm infants that may not be recognized using relative abundance alone. Very preterm neonates with sepsis have a significantly different longitudinal trajectory of microbiome development, which may, in part, extend to lower Bifidobacterium and higher Escherichia-Shigella abundance prior to the onset of sepsis. Bifidobacterium abundance appears to be particularly affected by antibiotic administration compared to other genera.},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Longitudinal Studies
Infant, Newborn
Male
*Sepsis/microbiology/drug therapy/therapy
Female
*Bifidobacterium/isolation & purification/genetics/growth & development
Feces/microbiology
Anti-Bacterial Agents/therapeutic use
RNA, Ribosomal, 16S/genetics
Infant, Premature
Bacteria/classification/genetics/isolation & purification
Dietary Supplements
Infant

@article {pmid40618170,
year = {2025},
author = {Shin, C and Ruhno, KE and Shin, JH and Hwang, S and Go, JR and Kang, M and Kim, HJ and Moon, JH and Kim, HJ},
title = {Spatial transcriptome analysis of myenteric plexus and intestinal epithelium of colon in patients with Parkinson's disease.},
journal = {Acta neuropathologica communications},
volume = {13},
number = {1},
pages = {146},
pmid = {40618170},
issn = {2051-5960},
support = {2022R1A2C2091254//National Research Foundation of Korea/ ; 11-2022-5010//Seoul National University Hospital/ ; },
mesh = {Humans ; *Myenteric Plexus/metabolism/pathology ; Male ; Female ; *Parkinson Disease/metabolism/genetics/pathology ; *Colon/metabolism/pathology ; Aged ; *Intestinal Mucosa/metabolism/pathology ; Middle Aged ; Gene Expression Profiling ; *Transcriptome ; alpha-Synuclein/metabolism ; },
abstract = {Alpha-synuclein (AS) accumulation is found in the nerve plexuses of the gastrointestinal tract in patients with Parknison's disease (PD). Moreover, alterations in microbiome composition and its metabolites were confirmed in the colon of patients with PD. However, there has been no study that evaluates transcriptomic alterations of the nerve plexus and intestinal epithelium simultaneously using in vivo tissue of patients with PD. Therefore, we aimed to investigate the gene expression profiles of the myenteric plexus and intestinal epithelium of the colon of patients with PD. Ten full-depth slides of paraffin-embedded surgical specimens of the colon or rectum from five patients with PD and five controls were included. AS accumulation was found in the myenteric plexus in all patients with PD. We performed spatial-specific transcriptomic profiling of the myenteric plexus and epithelium using the GeoMX Digital Spatial Profiler. Forty-one differentially expressed genes (DEGs) (36 up-regulated and 5 down-regulated) were identified in the myenteric plexus of patients with PD compared to controls. In the intestinal epithelium, 240 DEGs (81 up-regulated and 159 down-regulated) were identified. Pathway analysis showed upregulated response to type II interferon and lymphocyte activation, while downregulated cellular response to zinc and copper ions in the intestinal epithelium of patients with PD. In the myenteric plexus, neuroepithelial cell differentiation and axon development were upregulated. Network analysis showed the following key genes: and HLA-DRA, SERPINA1, and metallothioneins in the intestinal epithelium, and LAMP1, TUBB2A, and S100B in the myenteric plexus. This study suggests that inflammatory processes may occur in the intestinal epithelium, while neuronal regeneration mechanisms may be active in the myenteric plexus in patients with overtly developed PD. A spatial transcriptomic analysis of the brain and the gastrointestinal tract will enable a better understanding of the gut-brain axis in PD.},
}

Humans
*Myenteric Plexus/metabolism/pathology
Male
Female
*Parkinson Disease/metabolism/genetics/pathology
*Colon/metabolism/pathology
Aged
*Intestinal Mucosa/metabolism/pathology
Middle Aged
Gene Expression Profiling
*Transcriptome
alpha-Synuclein/metabolism

@article {pmid40618036,
year = {2025},
author = {Sato, K and Nakashima, A and Fukuda, S and Inoue, J and Kim, YG},
title = {Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {414},
pmid = {40618036},
issn = {1471-2180},
support = {JPMJSP2123//JST SPRING/ ; 2346//Sylff Research Grant/ ; JP23H02718//Japan Society for the Promotion of Science/ ; JP 23K18223//Japan Society for the Promotion of Science,Japan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Fasting ; Feces/microbiology/chemistry ; Animals ; *Bacteria/classification/genetics/isolation & purification ; Male ; Mice ; Immunoglobulin A/analysis ; Humans ; },
abstract = {Dietary nutrients are an important determinant of gut microbial composition (Asnicar et al, Nat Med 27:321-332, 2021; Arifuzzaman. et al, Nature 611:578-584, 2022; Bolte. et al, Gut 70:1287-1298, 2021). Commensal bacteria compete and cross-feed on host-derived nutrients to maintain stable gut microbial communities (Kolodziejczyk. et al, Nat Rev Microbiol. 17:742-753, 2019; Ma. et al, Gut Microbes 12:1785252, 2020). However, the changes to the gut bacteria induced by fasting are not well-defined. Here, we propose a powerful method to selectively and effectively increase specific gut bacteria by combining fasting and administration of microbiota-accessible carbohydrates (MACs). Fasting alters the gut microbial community structure, and the fasting + MAC intervention has profound effects on the gut microbiome with increased specific bacteria and fecal IgA levels than MAC administration alone. The changes in gut microbiota composition are specific to the type of MAC administered. We identified the most effective protocol to combine with fasting + MAC to increase the levels of specific bacteria such as Bifidobacterium. Overall, the integrating fasting with MACs effectively alters the gut microbiome, suggesting that fasting can prepare the environment for gut microbial modulation by MACs.},
}

*Gastrointestinal Microbiome/physiology
*Fasting
Feces/microbiology/chemistry
Animals
*Bacteria/classification/genetics/isolation & purification
Male
Mice
Immunoglobulin A/analysis
Humans

@article {pmid40617918,
year = {2025},
author = {Jamaluddin, NF and Brovkina, O and Nor Rashid, N and Al-Maleki, AR and Lim, YA and Tan, MP and Lee, SC and Duvallet, C and Corzett, CH and Alm, E and Groussin, M and Poyet, M and Ibrahim, F},
title = {Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24066},
pmid = {40617918},
issn = {2045-2322},
support = {RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; },
mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome ; *Life Style ; Male ; Female ; *Urbanization ; Adult ; Middle Aged ; Rural Population ; Urban Population ; Bacteria/classification/genetics ; Young Adult ; Diet ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is increasing evidence of distinct gut microbiome compositions between populations living industrialized and non-industrialized lifestyles worldwide. However, whether populations of Malaysia exhibit variations in their microbiome, and to what extent host lifestyle correlates with these variations, remains unclear. Malaysia's extensive geographical and sociocultural diversity provides a unique opportunity to explore how lifestyle and environmental exposures are associated with the human gut microbiome. Here, we characterized the gut microbiome of three populations in peninsular Malaysia, each representing different lifestyle contexts, and identified host factors associated with microbiome variation. Our findings suggest that lifestyle-related factors are strongly associated with differences in microbial community composition across populations. In particular, urban and rural individuals harbor gut microbiota with distinct community structures. We further identified specific taxa as potential microbial signatures of host lifestyle, with the genera Prevotella and Cryptobacteroides enriched in rural populations, while Phocaeicola, Vescimonas, and Megasphaera were more prevalent among urban individuals. In addition to lifestyle, demographic factors such as age, sex, and BMI were also associated with variation in the gut microbiome. This study highlights the influence of urbanization, lifestyle, and diet on the gut microbiome landscape of Malaysian populations and underscores the importance of considering sociocultural context in future microbiome research.},
}

Humans
Malaysia
*Gastrointestinal Microbiome
*Life Style
Male
Female
*Urbanization
Adult
Middle Aged
Rural Population
Urban Population
Bacteria/classification/genetics
Young Adult
Diet
RNA, Ribosomal, 16S/genetics

@article {pmid40617850,
year = {2025},
author = {Liu, Q and Fang, W and Zheng, P and Xie, S and Jiang, X and Luo, W and Han, L and Zhao, L and Lu, L and Zhai, L and Yu, DJ and Yang, W and Lin, C and Fang, X and Bian, Z},
title = {Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {129},
pmid = {40617850},
issn = {2055-5008},
support = {ITC RC/IHK/4/7//Health@InnoHK Initiative Fund of the Hong Kong Special Administrative Region Government/ ; S/N Ref: 2023-0045//Jockey Club Traditional Chinese Medicine-driven Mental Wellness Project/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/psychology/virology/complications ; *Gastrointestinal Microbiome ; *Depression/microbiology/virology ; Female ; Male ; *Bacteria/classification/virology/genetics/isolation & purification ; Prospective Studies ; *Anxiety/microbiology/virology ; Adult ; *Bacteriophages/genetics/classification/isolation & purification ; Hong Kong ; Middle Aged ; Virome ; Feces/microbiology/virology ; },
abstract = {Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities have been linked to IBS. Emerging data indicate that other intestinal organisms, including bacteriophages, are closely interlinked with the bacterial microbiota and their host, yet their collective role remains to be elucidated. Here, we analyze the gut multi-kingdom microbiota of 360 IBS patients from a prospective cohort study in Hong Kong, with participants phenotyped through psychological assessment. Our findings reveal significantly lower intra-community correlations in IBS patients compared to healthy controls and highlight unique taxa patterns associated with IBS and mental disorders. Utilizing multi-omic data alongside machine learning techniques, we successfully predicted psychiatric comorbidities in IBS, achieving an average AUC of 0.78. Notably, gut viruses emerged as significant contributors to our predictive model, indicating a vital role for bacteriophages in the gut microbiome of IBS patients. We found that lysogenic phages in IBS displayed a broader host range, with Bilophia containing the most abundant prophages. Our analysis further indicates that IBS patients with depression exhibited a higher prevalence of viral-encoded auxiliary metabolic genes, specifically those involved in the sulfur metabolic pathway related to ubiquinone biosynthesis. The gut virome is increasingly reported to play an important role in the pathogenesis of many diseases. The study provides a systematic characterization of the drivers of the gut viral community and further expands our knowledge of the distinct interaction of gut viruses with their prokaryotic hosts, which is critical for understanding the viral-bacterial environment in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/psychology/virology/complications
*Gastrointestinal Microbiome
*Depression/microbiology/virology
Female
Male
*Bacteria/classification/virology/genetics/isolation & purification
Prospective Studies
*Anxiety/microbiology/virology
Adult
*Bacteriophages/genetics/classification/isolation & purification
Hong Kong
Middle Aged
Virome
Feces/microbiology/virology

@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@article {pmid40617665,
year = {2025},
author = {Koutoukoglou, P and Mountzios, G},
title = {Beyond Programmed Death-Ligand 1: Gut Microbiome Composition as a Biomarker For First-Line Chemoimmunotherapy in Advanced NSCLC.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {20},
number = {7},
pages = {831-833},
doi = {10.1016/j.jtho.2025.04.011},
pmid = {40617665},
issn = {1556-1380},
}

@article {pmid40617511,
year = {2025},
author = {Arikawa, AY and Waterman, A and Mishra, SP and Labyak, C and Williams, C and Chaudhari, DS and Shukla, R and Kumar, V and Masternak, M and Holland, P and Golden, A and Dangiolo, M and Kociolek, J and Fraser, A and Agronin, M and Aymat, M and Yadav, H and Jain, S},
title = {Cognitive impairment is associated with alterations in diet quality and inflammatory biomarkers in older adults: a cross-sectional analysis of data collected from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.026},
pmid = {40617511},
issn = {1541-6100},
abstract = {BACKGROUND: Research suggests that gut inflammation and alterations in intestinal barrier function may be important mechanisms linking diet, systemic inflammation, and cognitive outcomes.

OBJECTIVE: The objective of this study was to explore the relationship between diet, cognitive health, and inflammatory markers in older adults. It was hypothesized that cognitive impairment would be associated with lower diet quality and higher levels of inflammatory markers.

METHODS: A cross-sectional analysis was conducted using data from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort. Participants aged 60 years and older were assessed for cognitive status using the Montreal Cognitive Assessment (MoCA), diet quality using the Healthy Eating Index-2020 (HEI-2020), and dietary inflammatory potential using the Dietary Inflammatory Index (DII). Inflammatory biomarkers were measured in plasma and stool samples, including interleukin (IL)-6, IL-1β, lipopolysaccharide binding protein (LBP), Toll-like receptor 4 (TLR4), and zonula occludens-1 (ZO-1).

RESULTS: Among 217 participants, 33.6% presented with cognitive impairment based on MoCA scores. There were no differences in DII and HEI-2020 scores between participants with and without cognitive impairment. The only significant finding related to the components of the HEI was a higher adequacy of dairy intake in those without cognitive impairment (54.8%) compared with those with cognitive impairment (44.4%, p=0.035). Key inflammatory markers, including IL-6, IL-1β, LBP, and TLR4, were elevated in those with cognitive impairment, while plasma ZO-1 levels were reduced. Stool calprotectin levels were notably higher in those with cognitive impairment, suggesting increased intestinal inflammation. There was a weak but significant correlation between stool calprotectin and DII score (rs=0.283, p=0.046).

CONCLUSION: The findings suggest that elevated inflammatory markers and disrupted intestinal barrier integrity may contribute to cognitive decline. These results highlight the need to develop dietary interventions to mitigate cognitive impairment through modulation of inflammation.},
}

@article {pmid40617320,
year = {2025},
author = {Lu, Y and Yi, F and Chen, W and Tan, X and Li, K and Yang, C and Lin, Y},
title = {Involvement of oxidative stress, lipid dysmetabolism and gut microbiol dysbiosis in oxaliplatin-induced fatty liver disease: evidence from a tree shrew model.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102645},
doi = {10.1016/j.clinre.2025.102645},
pmid = {40617320},
issn = {2210-741X},
abstract = {BACKGROUND: Oxaliplatin is cornerstone treatment for colorectal cancer, yet a significant proportion of patients develop drug-induced fatty liver disease (DILI). How it induces such liver injury is poorly understood and whether the gut microbiome is involved remains unknown.

METHODS: A male tree shrew model of oxaliplatin-induced DILI was established by six intraperitoneal injections (7 mg/kg every two weeks). During the early and late phases of liver injury, liver tissue was analyzed in terms of histopathology, oxidative stress and transcriptional profiling, while feces were subjected to microbial profiling based on 16S rRNA sequencing.

RESULTS: The model recapitulated key features of DILI, including severe hepatocyte steatosis and ballooning in the early phase after the final treatment, mild hepatic steatosis with sinusoidal dilatation in the late phase, and persistent hepatic oxidative stress during both phases. Transcriptional analysis of liver tissue identified 1503 differentially expressed genes (DEGs) between oxaliplatin-treated and control animals, of which 601 DEGs differed between treated animals in the early or late phases after the final treatment of DILI. Pathway enrichment revealed significant dysregulation in oxidative stress (e.g. NDUFA12, OSR1, MPO) and lipid metabolism (e.g., LDAH, ACACB, CH25H, LIPE) genes. Gut microbiota profiling showed an increase in the relative abundance of potentially harmful bacteria (e.g., Parabacteroides, Rikenella, Alistipes and Faecalitalea) and a concurrent decrease in the abundance of anti-oxidative bacteria (e.g., Lactococcus and Flavobacterium). Notably, abundance of several microbial genera in the gut correlated with liver expression of genes involved in oxidative stress and lipid metabolism as well as with levels of oxidative stress markers, and/or fat deposition in the liver.

CONCLUSION: Our results suggest that our tree shrew model can faithfully replicate key characteristics of oxaliplatin-induced fatty liver disease, and that such disease involves oxidative stress and lipid dysmetabolism in the liver as well as dysbiosis of microbiota in the gut.},
}

@article {pmid40617300,
year = {2025},
author = {Martin, EM and Xue, J and Smith, CJ},
title = {Effects of environmental toxicant exposures on oxytocin and vasopressin systems in the developing brain: Factors imparting risk and resilience.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {115723},
doi = {10.1016/j.bbr.2025.115723},
pmid = {40617300},
issn = {1872-7549},
abstract = {Environmental toxicants are increasingly prevalent worldwide and associated with numerous neurodevelopmental and psychiatric health outcomes. Exposure to these toxicants, particularly during gestation and the early postnatal period, alters maternal and offspring stress responses, inflammation, and behavioral outcomes. Oxytocin (OT) and arginine vasopressin (AVP) are highly conserved neuropeptides with myriad roles in the regulation of social behavior, stress responses, and more. While developmental stress is well known to impact OT and AVP systems, a growing body of literature suggests that early-life exposure to toxicants also impacts OT and AVP system development. Here we review the evidence demonstrating that perinatal exposures to environmental toxicants program developmental trajectories of the OT and AVP systems. Perinatal exposure to flame retardants, pesticides, plastics, and air pollution induces a variety of changes to OT and AVP systems in the brain, affecting the neuropeptides themselves as well as their primary central receptors, the oxytocin receptor (OTR) and the vasopressin receptor 1a (V1aR), respectively. Next, we discuss two biological mechanisms of action that may underlie the effects of toxicant exposure on OT and AVP: endocrine disruption and maternal immune activation. Finally, we explore key factors that promote either risk or resilience to toxicant exposures, including psychosocial experience, sex, the gut microbiome, and dosage/timing of exposure. Cumulatively, the literature reviewed suggests that preventing psychosocial stress to mothers during the perinatal period while promoting positive psychosocial experiences may lessen the impact of toxicants on offspring outcomes. Furthermore, the gut microbiome may be an important intermediary, and therefore target for intervention, between toxicant exposures and OT and AVP systems in the brain.},
}

@article {pmid40617206,
year = {2025},
author = {Mu, Y and Liu, L and He, J and Zhang, H and Yu, S and Zhu, Z and Huang, Y and Mou, M and Zhang, C},
title = {Investigating the variations in microbiome and volatilome characteristics of sauce-flavor Muqu across different grades and production rounds.},
journal = {Food chemistry},
volume = {492},
number = {Pt 1},
pages = {145394},
doi = {10.1016/j.foodchem.2025.145394},
pmid = {40617206},
issn = {1873-7072},
abstract = {Muqu is the starter of high-temperature Daqu; however, the mechanisms underlying its quality formation remain unclear. Therefore, the effects of grade and round on Muqu quality were investigated. Biochemical activities were closely associated with grade, while moisture and fat content were linked to round. The volatilome was also significantly influenced by grade, with levels of differential compounds such as trimethylpyrazine, 2,3-butanediol, and methyl hexanoate showing a positive correlation with grade. In contrast, bacterial and fungal diversities were regulated by grade and round, respectively, resulting in distinct interaction patterns within the co-occurrence network. Acidity and amino acid nitrogen levels were key factors driving community assembly, and Virgibacillus, Kroppenstedtia, Thermoactinomyces, Aspergillus, and Byssochlamys were identified as the primary flavor producers. Functional predictions indicated the pivotal role of bacterial communities in flavor synthesis and fungal communities in carbohydrate metabolism. These findings provide new insights into improving Daqu quality via the Muqu grading strategy.},
}

@article {pmid40617156,
year = {2025},
author = {Sola-Leyva, A and Pérez-Prieto, I and Di Nisio, V and Panagiotis-Deligiannis, S and Blanco-Rodríguez, L and Acharya, G and Saare, M and Papaikonomou, K and Damdimopoulou, P and Salumets, A and Altmäe, S},
title = {Assessing the ovarian microbiome: lack of a distinguishable microbial signature beyond contamination.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {3},
pages = {104988},
doi = {10.1016/j.rbmo.2025.104988},
pmid = {40617156},
issn = {1472-6491},
abstract = {RESEARCH QUESTION: Do the ovaries harbour commensal microbes?

DESIGN: Twenty-two ovarian tissue samples (cortex and medulla), six follicular fluid samples from gender-reassignment patients (GRP, n = 11) and five ovarian cortex tissue samples from Caesarean sections (n = 5), together with positive and negative controls, were analysed by bacterial 16S rRNA gene sequencing. Negative controls were obtained from saline storage buffer, air contaminants from the laboratory and operating room, and samples from clinicians and researchers handling the samples.

RESULTS: Of the 33 ovarian tissue and follicular fluid samples analysed, 63.6% did not result in any bacterial DNA amplification on PCR. As a result, only 1 out of 6 follicular fluid samples from GRP resulted in DNA amplification, while two ovarian cortex and four medulla samples from GRP, together with five ovarian samples from women undergoing Caesarean section, presented detectable bacterial DNA. Following sequencing, quality filtering and decontamination, negligible microbial reads were detected in these 12 samples. Despite strict protocols to avoid contamination during sample collection and processing, a high proportion of contaminant reads (30.3-100%, median 62.1%) were found in all the samples.

CONCLUSIONS: These findings do not support the existence of a specific ovarian microbiome in the ovaries of healthy participants. It can be concluded that the incidental detection of low-biomass bacterial genera is probably attributable to contamination.},
}

@article {pmid40617143,
year = {2025},
author = {Corrivetti, G and Monaco, F and Vignapiano, A and Marenna, A and Panarello, E and Di Gruttola, B and Landi, S and Malvone, R and Vecchi, C and Leo, S and Carmellini, P and Steardo, L and Solmi, M and Panella, R and Fasano, A},
title = {Precision medicine for depression: Improving treatment response and remission.},
journal = {Asian journal of psychiatry},
volume = {110},
number = {},
pages = {104585},
doi = {10.1016/j.ajp.2025.104585},
pmid = {40617143},
issn = {1876-2026},
abstract = {This review synthesises current knowledge to improve understanding of the pathophysiology of major depressive disorder (MDD) and optimise diagnostic, therapeutic and prognostic approaches. It examines the interplay between genetic, epigenetic, inflammatory, neurotransmitter and gut microbiome factors, together with environmental stressors and different clinical symptom presentations, in shaping MDD presentation and treatment response. Studies have revealed potential biomarkers predictive of treatment response, allowing differentiation of MDD subtypes and facilitating remission monitoring. While studies have identified potential biomarkers predictive of treatment response and enabling MDD subtype differentiation, significant challenges remain in achieving fully optimized therapeutic efficacy and widespread remission. A holistic, data-driven approach is key to addressing the complex aetiology of MDD, ultimately improving outcomes for patients and reducing the substantial burden of this prevalent disorder.},
}

@article {pmid40616950,
year = {2025},
author = {Jain, CK and Maurya, S and Singh, A},
title = {Bioinformatics-driven salivary microbial and functional profiling for identifying biomarkers in oral cancer and tobacco abusers in the Indian population.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106346},
doi = {10.1016/j.archoralbio.2025.106346},
pmid = {40616950},
issn = {1879-1506},
abstract = {OBJECTIVE: To investigate alterations in the salivary microbiome and its functional potential in Oral Squamous Cell Carcinoma (OSCC) patients, tobacco abusers, and healthy individuals in order to identify microbial biomarkers and gain insight into OSCC pathogenesis.

DESIGN: Saliva-derived 16S rRNA gene sequences from OSCC patients, tobacco users, and healthy controls were obtained from the Indian Biological Data Centre (IBDC). Taxonomic classification was performed using QIIME2, and functional prediction was conducted with MicFunPred. Alpha and beta diversity, differential abundance, and pathway enrichment analyses were used to compare microbial communities and functions among the groups.

RESULTS: OSCC samples showed significantly reduced alpha diversity and distinct microbial community profiles relative to healthy controls. Genera including Porphyromonas, Streptococcus, Rothia, and Parvimonas were enriched in OSCC and are associated with inflammation and carcinogenesis. Tobacco users exhibited increased microbial richness, with dominance of Prevotella, Veillonella, and Peptostreptococcus, indicative of adaptation to chemical exposure. Functional predictions in OSCC samples indicated enrichment in pathways related to bacterial chemotaxis, lipopolysaccharide biosynthesis, glycolysis, and DNA repair. Tobacco-associated microbiota showed elevated oxidative stress response and detoxification pathways.

CONCLUSIONS: Microbial dysbiosis and functional alterations in the oral microbiome are strongly associated with OSCC and tobacco use. The identification of disease-specific microbial signatures and pathways highlights the potential of the oral microbiome as a non-invasive biomarker and therapeutic target for precision medicine in OSCC, particularly in the Indian population.},
}

@article {pmid40616901,
year = {2025},
author = {Flygel, TT and Bargheet, A and Abotsi, RE and Claassen-Weitz, S and Simms, V and Hjerde, E and Mwaikono, KS and Mchugh, G and Hameiri-Bowen, D and Pettersen, VK and Ferrand, RA and Nicol, M and Cavanagh, JP and Flaegstad, T and Sovershaeva, E},
title = {Effect of long-term azithromycin treatment on gut microbial diversity in children and adolescents with HIV-associated chronic lung disease.},
journal = {EBioMedicine},
volume = {118},
number = {},
pages = {105832},
doi = {10.1016/j.ebiom.2025.105832},
pmid = {40616901},
issn = {2352-3964},
abstract = {BACKGROUND: HIV-associated chronic lung disease (HCLD) is common in children and adolescents growing up with HIV. The use of azithromycin (AZM) reduces the rate of acute respiratory exacerbations in this population, however, impact of this treatment on the gut microbiota and associations with blood-derived inflammatory markers have not been studied.

METHODS: Children and adolescents with HCLD in Harare, Zimbabwe and Blantyre, Malawi were recruited in a double-blind, placebo-controlled trial of once-weekly AZM or placebo for 48 weeks (BREATHE trial, NCT02426112). Rectal swabs were collected at inclusion (N = 346), 48 weeks (treatment end, N = 313), and 72 weeks (six months after treatment cessation, N = 244). The bacterial composition of fecal swabs was determined using 16S rRNA gene sequencing. Plasma biomarkers at inclusion and 48 weeks were measured using Luminex multiplex bead assay.

FINDINGS: At 48 weeks, bacterial α-diversity was significantly lower in the AZM group, with 27 bacterial genera showing differential abundance between the study groups. The placebo group exhibited higher interconnectivity between bacterial genera at 48 weeks compared to the AZM group. Correlations between the top seven differentially abundant genera and biomarkers observed at inclusion were no longer significant at 48 weeks in both groups. Depletion of Campylobacter persisted for six months after cessation of AZM treatment.

INTERPRETATION: Long-term AZM treatment in HCLD patients affects their gut bacterial composition at least 6 months after its cessation. The consequences of reduced bacterial diversity, such as altered interaction with the immune system and risk of resistance, need further investigation to understand how to optimise gut health during long-term antibiotic treatments.

FUNDING: The study was funded by the Norwegian Research Council and Helse Nord (HNF 1387-17).},
}

@article {pmid40616741,
year = {2025},
author = {Renton, N and Pillinger, MH and Toprover, M},
title = {Gout, Hyperuricemia, and the Intestinal Microbiome.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {40616741},
issn = {1573-2576},
abstract = {Gout is a disease of hyperuricemia (HU) leading to monosodium urate crystal deposition in the joint, resulting in inflammation and joint damage. Recently, efforts have been made to characterize the intestinal microbiome of patients who suffer from HU and gout, and pre-clinical studies have evaluated the utility of prebiotics and probiotics in alleviating gout. Herein we review recent notable studies addressing these topics. In brief, the "gouty" microbiome is characterized by reduced diversity, an elevated Bacteroides: Firmicutes ratio, and reduced presence of Akkermansia and Bifidobacterium. In anserine models, supplementation with Lactobacillus probiotic strains appears to reduce serum urate (SU) and HU-induced inflammation. Murine models suggest that the chicory-derived prebiotic inulin may reduce SU, and oral supplementation with the anti-inflammatory short-chain fatty acid butyrate may lower SU by enhancing urate excretion and alleviate HU-induced tissue inflammation. Many of these studies are limited by modest numbers of participants and/or incompletely documented experimental controls, and, in the case of animal models, questionable reproducibility in humans. Many studies have been geographically limited. There remains a need for more information regarding the features of the "gouty" microbiome in wider populations, as well as for additional well-controlled probiotic and prebiotic studies in more physiologically relevant animal models prior to clinical trials.},
}

@article {pmid40616291,
year = {2025},
author = {Facchin, S and Bonazzi, E and Tomasulo, A and Bertin, L and Lorenzon, G and Maniero, D and Zingone, F and Cardin, R and Barberio, B and Ghisa, M and Savarino, EV},
title = {Could modulation of the esophageal microbiome be the answer for eosinophilic esophagitis treatment?.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2530606},
pmid = {40616291},
issn = {1747-4132},
abstract = {INTRODUCTION: The oral and esophageal microbiota are gaining recognition for their significance in managing Eosinophilic Esophagitis (EoE). They serve as diagnostic biomarkers and therapeutic targets.

AREAS COVERED: The primary goal of EoE treatment is to alleviate symptoms such as dysphagia, heartburn, nausea, and chest pain. These symptoms are often associated with dysfunction of the esophageal barrier, closely linked to the esophageal microbiota. The composition of the esophageal microbiota can be affected by pharmacological treatments, particularly proton pump inhibitors, corticosteroids, and dietary interventions suggested for EoE management. As a result, the intestinal microbiota may also be influenced by these pharmacological approaches. Emerging research points to the potential of probiotic treatments as a complementary option to pharmacological therapy in the management of EoE. Publications linking "EoE" to "microbiome-microbiota" from 2013 to 2025 have been considered.

EXPERT OPINION: Further investigation into probiotics could expand the range of therapeutic options available alongside conventional treatments, potentially improving EoE remission rates, enhancing patient compliance, and reducing treatment-related side effects.},
}

@article {pmid40615889,
year = {2025},
author = {Park, K and Kim, Y and Kim, D and Oh, SM and Koo, TJ and Yoo, SM and Yoon, SH},
title = {Regulation of the tagatose catabolic gene cluster and development of a tagatose-inducible expression system in the probiotic Escherichia coli Nissle 1917.},
journal = {Microbial cell factories},
volume = {24},
number = {1},
pages = {158},
pmid = {40615889},
issn = {1475-2859},
support = {NRF-2022R1A2C2004292//National Research Foundation of Korea/ ; RS-2024-00401518//National Research Foundation of Korea/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; *Probiotics/metabolism ; *Hexoses/metabolism ; *Gene Expression Regulation, Bacterial ; *Multigene Family ; Escherichia coli Proteins/genetics/metabolism ; Humans ; },
abstract = {BACKGROUND: The probiotic Escherichia coli Nissle 1917 (EcN) is a promising microbial chassis for therapeutic and industrial applications. However, its broad utility is limited by a lack of reliable inducible gene expression systems that precisely control gene expression.

RESULTS: We developed a tagatose-inducible expression system in EcN using D-tagatose, a naturally occurring sugar with established safety in humans, as a metabolizable inducer. Through differential RNA sequencing and sequence analysis, we identified the key regulatory elements governing D-tagatose catabolism in EcN and demonstrated that the DeoR family regulator (TagR) functions as a tagatose-responsive repressor. The developed system exhibited a strong dose-dependent response to D-tagatose, ensuring uniform and tunable gene activation across cell populations. Additionally, a catabolite repression-enabled auto-induction strategy facilitated robust biomass accumulation, followed by targeted protein production. This expression system was successfully applied to overexpress recombinant proteins under both aerobic and anaerobic conditions.

CONCLUSIONS: D-Tagatose is a naturally occurring low-calorie sugar that can serve as an inducer in vivo, including within the human gut microbiome. Thus, the tagatose-inducible expression system provides EcN with an additional tunable option for gene regulation, which may be valuable in applications such as synthetic biology and metabolic engineering.},
}

*Escherichia coli/genetics/metabolism
*Probiotics/metabolism
*Hexoses/metabolism
*Gene Expression Regulation, Bacterial
*Multigene Family
Escherichia coli Proteins/genetics/metabolism
Humans

@article {pmid40615864,
year = {2025},
author = {Kim, H and Chae, Y and Cho, JH and Song, M and Kwak, J and Doo, H and Choi, Y and Kang, J and Yang, H and Lee, S and Keum, GB and Wattanaphansak, S and Kim, S and Kim, HB},
title = {Understanding the diversity and roles of the canine gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {95},
pmid = {40615864},
issn = {1674-9782},
support = {RS-2023-00230754//Rural Development Administration/ ; },
abstract = {The canine gut microbiome plays a vital role in overall health and well-being by regulating various physiological functions, including digestion, immune responses, energy metabolism, and even behavior and temperament. As such, a comprehensive understanding of the diversity and functional roles of the canine gut microbiome is crucial for maintaining optimal health and well-being. In healthy dogs, the gut microbiome typically consists of a diverse array of bacterial phyla, including Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria. These microbial communities form a complex ecosystem that interacts with the host to support canine health and homeostasis. A well-balanced microbiome, known as eubiosis, represents an optimized microbial composition that enhances host health and metabolic functions. Eubiosis is shaped by interactions between host physiology and environmental factors. However, dysbiosis, a disruption of eubiosis, can contribute to various health issues, such as weight fluctuations, metabolic disorders, and behavioral changes. Maintaining eubiosis in the canine gut microbiome requires customized management strategies that consider both physiological traits and environmental influences. In this review, we explored the structure and function of the canine gut microbiome, with particular emphasis on its role in health and the key factors that influence and support its maintenance.},
}

@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}

@article {pmid40615821,
year = {2025},
author = {Upadhyay, P and Kumar, S and Tyagi, A and Tyagi, AR and Barbhuyan, T and Gupta, S},
title = {Gut Microbiome rewiring via fecal transplants: Uncovering therapeutic avenues in Alzheimer's disease models.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {39},
pmid = {40615821},
issn = {1471-2202},
support = {File no.R.12014/20/2018//Department of Health Research, India/ ; DBT Core grant//National Institute of Immunology New Delhi India/ ; },
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiome in Alzheimer's disease (AD) pathogenesis, yet the underlying mechanisms remain elusive. This study elucidates the bidirectional relationship between gut microbiota and AD using fecal microbiota transplantation (FMT) in a mouse model.

RESULT: Through meticulous experimentation, we conducted reciprocal FMT between AD (5xFAD) and healthy (C57BL/6) mice to unravel the impact of gut microbiome alterations on cognitive function and neuroinflammation. FMT from 5xFAD to C57BL/6 mice induced profound memory impairment and cognitive deficits, accompanied by elevated inflammatory cytokine levels, oxidative stress markers, and systemic inflammation, as evidenced by increased plasma cytokines. Conversely, transplanting healthy microbiota into 5xFAD mice yielded remarkable behavioral improvements, including enhanced spatial memory performance in the Morris water maze, directly correlating with cognitive recovery. Our findings underscore the pivotal role of the gut microbiome in AD pathogenesis and offer a promising therapeutic avenue.

CONCLUSION: Targeted modulation of the gut microbiome through strategies like FMT may offer potential benefits in Alzheimer's disease by influencing neuroinflammation, oxidative stress, and cognitive function. This comprehensive study provides novel insights into the gut-brain axis dynamics and paves the way for innovative microbiome-based interventions in AD management.},
}

@article {pmid40615170,
year = {2025},
author = {Chowdhury, R and Maddheshiya, A and Taneja, S and Bhandari, N and Majumder, PP and Strand, TA and Pandey, RM and Kurpad, AV and Mukherjee, S},
title = {Impact of an Integrated Intervention Package During Preconception, Pregnancy, and Early Childhood on the Gut Microbiome at Six Months of Age: Findings from the Women and Infants Integrated Growth Study (WINGS) Randomized Controlled Trial.},
journal = {The Journal of nutrition},
volume = {155},
number = {7},
pages = {2355-2366},
doi = {10.1016/j.tjnut.2025.04.016},
pmid = {40615170},
issn = {1541-6100},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; Infant ; Adult ; Young Adult ; Adolescent ; Male ; Feces/microbiology ; *Preconception Care ; },
abstract = {BACKGROUND: The infant gut microbiome is essential for healthy growth and development. However, limited research has explored how interventions targeting maternal and infant health, nutrition, and psychosocial conditions during preconception, pregnancy, and early childhood impact microbiome development. To address this research gap and better understand the potential impact of such interventions, this study was designed to evaluate their effects on the infant gut microbiome.

OBJECTIVE: The aim was to evaluate the effects of an integrated intervention package on infant gut microbiome at 6 mo of age compared with routine care.

METHODS: The study was embedded in a randomized factorial trial involving women aged 18-30 y. Participants were randomly assigned to receive either a preconception intervention package or routine care until pregnancy. Pregnant women were then randomly assigned to receive a pregnancy and early childhood intervention package or routine care. The intervention included health care for growth-related conditions, nutrition, water, sanitation, and hygiene (WASH), and psychosocial care. Stool samples from 392 infants (185 from the preconception, pregnancy, and early childhood intervention group and 207 from the routine care group) were collected at 6 mo, followed by microbiome DNA isolation and high-throughput sequencing of the V3-V4 region of 16S rRNA gene. Generalized linear models were used to estimate the mean relative abundance of core gut microbiome phyla, genera, and species between the intervention and routine care groups.

RESULTS: Infants in the group who received preconception, pregnancy, and early childhood intervention had a significantly lower mean relative abundance of Klebsiella genus under the Pseudomonadota phylum (45% lower; 95% confidence interval [CI]: 18, 63) and Klebsiella pneumoniae species (38% lower; 95% CI: 8, 59) compared with routine care group. In contrast, the relative abundance of Megasphaera (72% higher; 95% CI: 7, 175), Prevotella (72% higher; 95% CI: 3, 187), and Bifidobacterium breve (34% higher; 95% CI: 2, 79) was significantly higher in the group received preconception, pregnancy and early childhood intervention compared with routine care.

CONCLUSIONS: The findings indicate that improving maternal and infant health, nutrition, and psychosocial conditions enhances the relative abundance of beneficial gut bacteria at 6 mo of age, supporting healthy growth and development. This trial was registered at Clinical Trials Registry-India as CTRI/2020/10/028770; https://ctri.nic.in/Clinicaltrials/advsearch2.php.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
Infant
Adult
Young Adult
Adolescent
Male
Feces/microbiology
*Preconception Care

@article {pmid40615087,
year = {2025},
author = {Wang, H and Liang, Y and Boor, PJ and Khanipov, K and Zhang, Y and Yu, X and Ambati, CSR and Putluri, N and Khan, MF},
title = {Protective role of dietary short chain fatty acid propionate against autoimmune responses and pathology of systemic lupus erythematosus in MRL-lpr mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.031},
pmid = {40615087},
issn = {1541-6100},
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease (AD) that affects multiple organs, including skin and kidney. The etiology of SLE remains unclear but involves hormonal, environmental and genetic factors. Environmental factors, such as diet and microbiota-derived metabolites, among which short chain fatty acids (SCFAs) are major players, can influence AD pathogenesis.

OBJECTIVE: This study investigates the involvement of SCFAs in the pathogenesis of SLE and further investigated the effect of propionate (PA) supplementation on SLE disease outcome in MRL-lpr mice.

METHODS: Cecal SCFAs from mouse models with varying degrees of SLE disease activities (C57BL/6, MRL+/+ and MRL-lpr) were determined by LC-MS analysis. Five-week-old MRL-lpr mice were supplemented with PA (200 mM, via drinking water) for 6 weeks, and assessed autoimmunity and disease markers.

RESULTS: LC-MS analysis of cecal SCFAs showed a significant decrease of PA in MRL-lpr mice (p < 0.001). PA treatment ameliorated the autoimmune response, evident from reduced serum autoantibodies (p < 0.05 for both ANA and anti-dsDNA) and a significant alleviation of glomerulonephritis (p < 0.05). Furthermore, it restored the imbalances in gut microbiome composition and SCFAs, especially propionate (p < 0.01). Additionally, PA treatment resulted in decreased splenic activated CD4 T cells (p < 0.05) and alterations in renal inflammatory signaling pathways.

CONCLUSIONS: Our findings support the beneficial effects of propionate in alleviating SLE, and therapeutic potential of propionate or propionate-producing bacteria for SLE.},
}

@article {pmid40615083,
year = {2025},
author = {Duan, Y and Li, Y and Xu, C and Wang, W and Wang, X and Zheng, W and Hsing, JC and Wu, J and Myers, A and Hsing, AW and He, W and Zhu, S},
title = {Fried food consumption-related gut microbiota is associated with obesity, fat distribution and cardiometabolic diseases: results from two large longitudinal cohorts with sibling comparison analyses.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.025},
pmid = {40615083},
issn = {1938-3207},
abstract = {BACKGROUND: In prospective cohort studies, the relationship between fried food consumption, gut microbiota, obesity, and cardiometabolic diseases remains unknown.

OBJECTIVE: We aimed to explore associations of fried food consumption with gut microbiota and associations of fried food consumption-related microbiota with obesity and related disorders.

METHODS: We analyzed 6,637 individuals from the WELL-China cohort (baseline 2016-2019) and 3,466 from the Lanxi cohort (baseline 2017-2019), with follow-up until June 24, 2024. Face-to-face interviews provided data on fried food consumption and other covariates. Analysis of 16S rRNA data from fecal samples collected at baseline identified microbial genera. Body composition was evaluated using dual-energy X-ray absorptiometry (DXA). The Microbiome Multivariable Associations with Linear Models (MaAsLin) helped identify genera associated with frequency of fried food consumption in the cross-sectional analysis. Cox regression models examined the relationship of fried food consumption-related microbiota with cardiometabolic diseases during follow-up. Sibling comparison analyses were used to control for unmeasured familial confounders using the between-within (BW) model.

RESULTS: Twenty-five microbial genera were significantly associated with fried food consumption frequency. Using these genera, we constructed a fried food consumption-related microbiota index. Meta-analysis of both cohorts found a positive relationship of this index with overall adiposity measures (BMI) (β coefficient, 0.26; 95% confidence interval (CI), 0.19-0.32) and central fat distribution parameters (including android-gynoid fat ratio (β, 1.48; 95% CI, 1.14-1.82)). Longitudinal analyses indicated that a higher fried food consumption-related microbiota index was linked to a higher risk of developing cardiometabolic diseases, with adjusted hazard ratios (95% CI) of 1.16 (1.07-1.27) for diabetes and 1.16 (1.06-1.26) for major adverse cardiovascular events. Sibling comparison analyses yielded similar results.

CONCLUSIONS: Fried food consumption-related microbiome is associated with a higher risk of obesity, central fat distribution, and cardiometabolic diseases, emphasizing the importance of dietary choices in the management and prevention of chronic diseases.},
}

@article {pmid40615058,
year = {2025},
author = {Vanhatalo, A and L'Heureux, JE and Black, MI and Blackwell, JR and Aizawa, K and Thompson, C and Williams, DW and van der Giezen, M and Winyard, PG and Jones, AM},
title = {Ageing modifies the oral microbiome, nitric oxide bioavailability and vascular responses to dietary nitrate supplementation.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.07.002},
pmid = {40615058},
issn = {1873-4596},
abstract = {This study evaluated whether changes in the oral microbiome in response to dietary nitrate and antiseptic mouthwash treatments were related to changes in nitric oxide bioavailability and vascular function. Thirty-nine young (18-30 years) and thirty-six older (67-79 years) males and females completed a placebo-controlled, double-blind cross-over intervention including three 2-week conditions separated by 2-week washouts: placebo beetroot juice (PL), nitrate-rich beetroot juice (BR) and antiseptic mouthwash (MW). The oral microbiomes of young and older adults responded differently to BR (post BR non-metric multidimensional scaling P=0.01), while the oral microbiomes of both age groups were unaffected by PL and MW interventions. Older people, who had elevated baseline mean arterial pressure (MAP; 95±9 mmHg) compared to young adults (87±7 mmHg, P<0.001), showed decreased brachial MAP (-4±4 mmHg, P=0.003) after BR while this effect was absent in the young. Flow mediated dilatation (FMD) variables were not affected by the interventions in older adults, while in the young there was a difference in changes (from pre to post) in ΔFMD% between the MW and BR conditions (P=0.04). Decreased blood pressure in older adults correlated with increased plasma nitrite concentration (change in central MAP vs. [NO2[-]] r=-0.41, P=0.02), which in turn correlated with decreases within the co-occurring module of bacteria dominated by the genus Prevotella (P. intermedia r=-0.72, P=0.001; P. dentalis r=-0.88, P<0.0001; Crassaminicella sp. SY095 r=-0.81, P<0.0001). Greater blood pressure benefits from supplemental dietary nitrate in older compared to younger people are mediated primarily by the suppression of potentially harmful oral bacteria, that have been associated with ammonia production.},
}

@article {pmid40614920,
year = {2025},
author = {Yadav, S and Raj, RG},
title = {Parkinson's disease and the gut microbiota connection: unveiling dysbiosis and exploring therapeutic horizons.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.07.003},
pmid = {40614920},
issn = {1873-7544},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder marked by dopaminergic neuronal loss, α-synuclein aggregation, and sustained neuroinflammation. Emerging evidence supports the gut-brain-microbiota axis as a pivotal player in the disease's pathogenesis. Dysbiosis, disruptions in the gut microbial composition, has been consistently observed in individuals with PD, with notable reductions in beneficial, short-chain fatty acid-producing bacteria and elevations in pro-inflammatory microbial species. These alterations contribute to increased intestinal permeability, systemic inflammation, and heightened neuroinflammatory responses that may drive α-synuclein misfolding and dopaminergic degeneration. In addition, microbial metabolites, including lipopolysaccharides and amyloid proteins such as curli, may promote neurodegeneration via immune and molecular mimicry pathways. Recent advances highlight the bidirectional influence of the microbiota-gut-brain axis on PD symptoms, ranging from motor deficits to non-motor features like constipation, depression, and cognitive decline. Several microbiota-modulating interventions, including probiotics, prebiotics, dietary strategies, antibiotics, and fecal microbiota transplantation, have demonstrated neuroprotective potential in both preclinical and clinical contexts. However, inter-individual variability, methodological heterogeneity, and the absence of longitudinal, multi-omics-integrated studies limit current understanding. The gut microbiome also holds promise as a non-invasive biomarker for early PD detection and prognosis, though standardization remains a challenge. Future research must clarify causal mechanisms, optimize therapeutic delivery, and integrate genetic, metabolic, and environmental data to advance precision medicine approaches. This review consolidates current knowledge on gut microbiota's role in PD pathophysiology and therapeutic innovation, providing a roadmap for future research directions.},
}

@article {pmid40614884,
year = {2025},
author = {Dong, TS and Jann, K and Wang, DJ and Church, A},
title = {Understanding Whole Person Systems in Brain-Gut-Microbiome Research Through Ultra-High-field MRI Imaging.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121360},
doi = {10.1016/j.neuroimage.2025.121360},
pmid = {40614884},
issn = {1095-9572},
abstract = {The brain-gut-microbiome (BGM) axis regulates interoception, metabolism, and immunity, with dysfunction linked to IBS, obesity, and mood disorders. Ultra-high-field (UHF) MRI advances neural imaging, enhancing resolution of vagal and spinal circuits mediating gut-brain communication. UHF enables real-time tracking of interventions like vagus nerve stimulation and probiotics, linking microbiome shifts to neural adaptations. Despite challenges like signal distortions, innovations in coil design are improving imaging fidelity. Integrating neuroimaging with multi-omic profiling fosters a systems-level approach, advancing personalized therapies for BGM disorders. This commentary underscores UHF MRI's transformative potential in bridging neuroscience, microbiome science, and clinical applications.},
}

@article {pmid40614851,
year = {2025},
author = {Yang, X and Huang, X and Zheng, B and Gao, F and He, L and Xu, Q},
title = {Natural-Setting Evidence of Stochastic-to-Deterministic Gut Microbiome Assembly and Metabolic Shifts in Regenerating Tropical Sea Cucumber Stichopus monotuberculatus.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122260},
doi = {10.1016/j.envres.2025.122260},
pmid = {40614851},
issn = {1096-0953},
abstract = {Holothurians exhibit a distinctive ability to eviscerate and regenerate internal organs, making them an ideal model for investigating host-microbe interactions. This study examined the dynamics of the gut microbiome and the associated metabolome during intestinal regeneration in the tropical sea cucumber Stichopus monotuberculatus under natural conditions. Through a combination of 16S rDNA sequencing and GC-MS-based metabolomics, we determined stage-specific shifts in gut microbial communities and metabolite profiles. Early regeneration was characterized by a stochastic influx of environmental microbes, low microbial network connectivity, and high metabolite-microbe correlation complexity, which suggested that the host relied on metabolic signals to coordinate the initial colonization of a diverse microbial community sourced from environment. As regeneration advanced, the microbial network grew increasingly cohesive, environmental contribution diminished, and metabolite-microbe correlation decreased. The reestablished gut microbiome exhibited no significant structural differences compared to pre-evisceration communities. This process reflected a transition from stochastic recruitment to host-filtered deterministic assembly, ultimately restoring a stable microbiome. Core microbial taxa such as Roseburia, Faecalibacterium, and Ruegeria were associated with pathways related to nutrient provisioning, energy production, and immune regulation, suggesting their potential contributions to intestinal recovery. Metabolomic analysis revealed significant alterations in amino acid, lipid, and carbohydrate metabolism, highlighting the functional integration between the gut bacteria and regenerated host tissue. Our findings provide novel insight into the interactions among host, microbe, and environment during gut microbiome assembly, as well as highlight the balance between stochastic and deterministic factors in the formation of marine holobiont communities.},
}

@article {pmid40614836,
year = {2025},
author = {Yu, J and Zhu, H and Yu, X and Liu, Y and Zhang, J and Jiang, L and Zhang, X},
title = {Calcitriol/Vitamin D Receptor Ameliorates Fructose-Induced Enteritis-Hepatitis Axis Dysregulation in Mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110017},
doi = {10.1016/j.jnutbio.2025.110017},
pmid = {40614836},
issn = {1873-4847},
abstract = {Emerging evidence associates excessive fructose consumption with intestinal inflammation and metabolic dysfunction-associated steatotic liver disease (MASLD), though the underlying mechanisms remain elusive. This preclinical study systematically investigated the therapeutic potential of calcitriol/vitamin D receptor (VDR) signaling in counteracting fructose-induced gut-liver axis dysregulation using female C57BL/6J mice. Experimental groups included: (1) Control (C), (2) Fructose (F; 20% w/v fructose water for 8 weeks), (3) Fructose+Calcitriol (F+V; 300 ng/kg calcitriol gavage during weeks 4-8), and (4) Calcitriol alone (V). Key findings revealed that chronic fructose exposure induced gut microbiota dysbiosis (characterized by decreased Firmicutes/Bacteroidetes ratio), compromised intestinal barrier integrity through downregulation of tight junction proteins, depleted secretory cells (Goblet/Paneth cells), and triggered apoptosis with concomitant elevation of pro-inflammatory cytokines (TNF-α, IL-6). These intestinal alterations culminated in endotoxemia-mediated hepatic inflammation and fibrogenesis, accompanied by persistent NF-κB pathway activation. Notably, calcitriol intervention significantly restored VDR expression, enhanced autophagic flux, stimulated mucin/antimicrobial peptide production, and suppressed NF-κB-mediated inflammatory responses. In vitro validation using Caco2 and RAW264.7 cells demonstrated that VDR activation effectively reversed fructose-impaired autophagy and NF-κB hyperactivation. Microbiome analysis further indicated calcitriol's partial normalization of fructose-induced microbial shifts, suggesting microbiota-mediated mechanisms. Collectively, these findings establish that calcitriol/VDR signaling mitigates fructose-driven gut-liver axis dysfunction through coordinated regulation of autophagy, mucosal defense systems, and inflammatory pathways. This mechanistic framework positions the VDR pathway as a promising therapeutic target for enteritis-hepatitis axis disorders, warranting further clinical investigation.},
}

@article {pmid40614808,
year = {2025},
author = {He, S and Chen, C and Cao, L and Nauta, A and Liu, X and Chen, H and Spoelstra, J and Yang, B},
title = {Metabolic diversity and competitive interactions of infant-derived bifidobacteria in human milk oligosaccharides and galacto-oligosaccharides utilization.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26559},
pmid = {40614808},
issn = {1525-3198},
abstract = {Human milk oligosaccharides (HMO) play a pivotal role in shaping the infant gut microbiome and immune system, primarily by selectively promoting Bifidobacterium species. Although the metabolic pathways of individual bifidobacterial strains for HMO are well-characterized, competitive interactions among multiple strains under single-HMO conditions remain poorly understood. Here, we evaluated metabolic capabilities of 15 infant-derived Bifidobacterium strains on 3 substrates: 2'-fucosyllactose (2'-FL), lacto-N-tetraose (LNT), and high-purity galacto-oligosaccharides (GOS-HP). Monoculture and mixed-culture analyses were conducted using growth kinetics, substrate consumption assays, and genomic profiling. Monoculture results demonstrated most strains exhibited robust growth on LNT and GOS-HP, whereas 2'-FL utilization varied. Genomic analysis indicated efficient HMO metabolism correlated with glycosyl hydrolase gene diversity and copy numbers. In mixed cultures, B. dentium initially dominated through monosaccharide consumption but was subsequently outcompeted by B. longum ssp. infantis and B. breve, highlighting oligosaccharide-driven competition. The LNT mixed culture resulted in a bifidobacterial community composition resembling that of breastfed infants. These findings guide oligosaccharide selection for infant formula design to better emulate human milk's microbiome-modulating benefits.},
}

@article {pmid40614713,
year = {2025},
author = {Cowan, CM and Pietras, EM},
title = {From symbiote to bad neighbor: The intestinal microbiome as a driver of CHIP.},
journal = {Cell stem cell},
volume = {32},
number = {7},
pages = {1036-1037},
doi = {10.1016/j.stem.2025.06.003},
pmid = {40614713},
issn = {1875-9777},
mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Hematopoietic Stem Cells/metabolism ; *Clonal Hematopoiesis ; Mice ; },
abstract = {Hematopoietic stem cells (HSCs) with mutations that can cause clonal hematopoiesis of indeterminate potential (CHIP) accumulate during aging. Agarwal et al.[1] demonstrate in Nature that intestinal barrier permeability increases with age and enables the microbial metabolite ADP-heptose to reach the bone marrow, thus driving the expansion of DNMT3A-mutant HSCs.},
}

*Gastrointestinal Microbiome
Humans
Animals
*Hematopoietic Stem Cells/metabolism
*Clonal Hematopoiesis
Mice

@article {pmid40614655,
year = {2025},
author = {Ghosh, R and Sui, P and Fritze, D and Fernandez, S and Torres, A and Woodworth, J and Cigarroa, FG and Halff, GA and Kumar, AP},
title = {Characterization of metabolomic associated with pancreatic cancer patients with overweight and obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {240-251},
doi = {10.1016/j.clnu.2025.06.015},
pmid = {40614655},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The near equal incidence and mortality rates of pancreatic cancer, combined with projections that by 2050 pancreatic cancer will be the second-most fatal cancer, underscore the need to identify patients with early disease and thus interrupt this trajectory. Obesity, weight gain and waistline have been implicated in increasing the risk of pancreatic cancer. Factors such as inflammation, insulin resistance, and changes in intestinal microbiome have been suggested to be involved in obesity. Although metabolomic analyses of pancreatic cancer patients have established correlations between phospholipids, lysophospholipids with treatment outcomes, the association between metabolites, obesity, and pancreatic cancer remains largely understudied. We hypothesized that global metabolomic profile of obese and overweight pancreatic cancer patients will be different compared with healthy weight subjects with no cancer.

METHODS: Global metabolic profiles were determined in obese and overweight pancreatic cancer patients compared with healthy weight subjects using ultrahigh performance liquid chromatography-tandem mass spectroscopy.

RESULTS: Analysis of the data using the Benjamini & Hochberg method to control the false discovery rate revealed statistically significant changes in branched chain amino acids, lipid metabolites including monoacyl glycerol, and fructose in overweight/obese pancreatic cancer patients relative to healthy weight.

CONCLUSION: Our findings suggest that metabolomic pathways as potential targets for high-risk pancreatic cancer patients.},
}

@article {pmid40614652,
year = {2025},
author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T},
title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105488},
doi = {10.1016/j.psj.2025.105488},
pmid = {40614652},
issn = {1525-3171},
abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.},
}

@article {pmid40614627,
year = {2025},
author = {Pecyna, P and Bykowska-Derda, A and Gabryel, M and Mankowska-Wierzbicka, D and Nowak-Malczewska, DM and Jaskiewicz-Rajewicz, K and Jaworska, MM and Grzymislawski, M and Dobrowolska, A and Czlapka-Matyasik, M and Gajecka, M},
title = {Blautia spp. in the gut microbiome: Its relation to dietary choices and to the nutritional status of patients with irritable bowel syndrome.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {138},
number = {},
pages = {112836},
doi = {10.1016/j.nut.2025.112836},
pmid = {40614627},
issn = {1873-1244},
abstract = {OBJECTIVES: Uncontrolled growth of certain Blautia spp. species could be associated with symptoms identified in patients with irritable bowel syndrome (IBS). As no studies have thus far focused on the relationship between nutrition habits, body composition, and the abundance of Blautia spp. in patients with IBS, this study aimed to determine the above-mentioned aspects.

METHODS: The gut microbiota of patients with IBS (n = 73) and a control group (n = 54) were subjected to 16S ribosomal RNA sequencing. Food frequency intake, physical activity, and socioeconomic status were measured by the Dietary Habits and Nutrition Beliefs Questionnaire KomPAN. Body composition was assessed by the air plethysmography method (BodPod, Life Measurement Inc., Concord, CA, USA).

RESULTS: Blautia spp. was more abundant in the gut microbiota of patients with IBS than in control participants. In patients with IBS, a relation was observed between the frequency of fruit intake and Blautia spp. abundance (odds ratio [OR] = 0.35; 95% confidence interval [95% CI]: 0.12-1.01; P = 0.04). When comparing all study participants, individuals with a high relative Blautia spp. abundance consumed white bread more frequently than the remaining participants (OR = 2.26; 95% CI: 1.03-4.96; P = 0.04). In turn, the high-frequency intake of wholegrain bread and legumes was related to decreased Blautia spp. abundance OR = 0.29; 95% CI: 0.10-0.94; P = 0.03 and OR = 0.38; 95% CI: 0.17-0.83; P = 0.01, respectively). A body fat percentage over 40% was related to high Blautia spp. abundance (OR = 2.85; 95% CI: 0.99-8.16; P = 0.04).

CONCLUSIONS: A diet high in wholegrain bread, legumes, and vegetables may influence Blautia spp. abundance in the gut microbiota. High levels of Blautia spp. in the gut are also related to body composition.},
}

@article {pmid40614495,
year = {2025},
author = {Su, X and Liu, M and Chen, Y and Feng, D and Xu, J and He, Y},
title = {Microplastics aging potentially enlarge the ecological risk to wetland sediments as revealed by their interactive effects on γ-HCH dissipation and methane production.},
journal = {Water research},
volume = {285},
number = {},
pages = {124137},
doi = {10.1016/j.watres.2025.124137},
pmid = {40614495},
issn = {1879-2448},
abstract = {Microplastics (MPs) have garnered global concern, yet the environmental implications of their aging remain poorly understood. Especially, their interactions with co-occurring pollutants and impacts on biogeochemical processes in wetland sediments require further investigation. Through microcosm experiments, this study systematically elucidated the differential effects of pristine vs. aged MPs on γ-hexachlorocyclohexane (γ-HCH) behavior and methanogenesis. Aged MPs exhibited enhanced γ-HCH adsorption (666.7 vs. 500.0 mg kg[-1] for pristine MPs), yet paradoxically inhibited γ-HCH dissipation in wetland sediments. This demonstrates that previous studies might oversimplify the interaction between MPs and pollutants. Concurrently, Dhc functional gene abundance on aged MP-surface biofilms declined sharply from 3015.4 to 811.4 copies g[-1] dw over 60 days, suggesting impaired functional microorganisms. Notably, aged MPs amplified CH4 production (1.64 ± 0.10 vs. 1.25 ± 0.15 mg kg[-1] day[-1] pristine MPs) and H2O2 generation (2.62 ± 0.12 vs. 2.06 ± 0.05 mmol L[-1] pristine MPs), with reduced microbial complexity and stability. Mechanistically, aging altered MP surface properties, selectively enriching mcrA functional genes and methanogenic archaea (Methanomassiliicoccus and Methanosarcina). These findings show aged MPs in suppressing pollutant dissipation (γ-HCH) while accelerating elemental cycling (CH4), driven by reactive oxygen species and microbiome shifts. Given the widespread occurrence of aged MPs in wetlands, this study underscores their underappreciated yet critical influence on wetland sediment biogeochemistry, urging prioritized research to mitigate their cascading potential risks.},
}

@article {pmid40613995,
year = {2025},
author = {Ghamari, M and Sabzi, S and Rajabi, E and Khodadadi, G and Navidifar, T and Sadeghi, Z and Bostanghadiri, N},
title = {Probiotics, Prebiotics, Synbiotics, Postbiotics, and Bioactive Agents in Modulating Harmful Oral Biofilms.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40613995},
issn = {1867-1314},
abstract = {Oral biofilms are intricate microbial communities that can enhance oral health, yet their equilibrium is susceptible to disruption, leading to oral infectious diseases. The most prevalent of these are dental caries, periodontitis, and peri-implant infections. The formation of pathogenic biofilms is the primary cause of these diseases, and their resistance to antimicrobial agents and immune responses poses significant treatment challenges. Researchers have recently implemented microbiome-based strategies, including probiotics, prebiotics, synbiotics, and postbiotics, to modulate biofilm composition and restore microbial equilibrium. Probiotics exert their health effects by competitively inhibiting pathogenic bacteria, producing antimicrobial compounds, and interacting with the immune system. Moreover, prebiotics can selectively stimulate beneficial bacteria, while synbiotics and postbiotics increase these effects using synergistic mechanisms. Recent studies suggest that integrating these strategies into oral healthcare can offer effective, non-invasive approaches to manage biofilm-related oral infections. Notwithstanding the challenges, issues pertaining to strain-specific efficacy, probiotic viability, and long-term colonization remain to be addressed. This review has collated recent research in this area and highlights promising therapeutic directions for improving oral health outcomes.},
}

@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}

@article {pmid40613843,
year = {2025},
author = {Huang, R and Jin, X and Liu, Q and Bai, X and Wu, Y and Wang, Y and He, X and Jiang, Z and Wang, L and Zhu, W},
title = {Genetic evidence for causal links between diet, gut microbiota, and hepatobiliary cancer: a Mendelian randomization study.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {100},
pmid = {40613843},
issn = {2191-0855},
support = {81874182//National Natural Science Foundation of China/ ; 81874056//National Natural Science Foundation of China/ ; 201940043//the Public Health Bureau Foundation of Shanghai/ ; 202240240//the Public Health Bureau Foundation of Shanghai/ ; 2022YFE0125300//National Key Research and Development Plan of the Ministry of Science and Technology/ ; 22ZR1413300//Shanghai Natural Science Foundation Project/ ; },
abstract = {Emerging evidence suggests a complex interplay among dietary habits, gut microbiota, and hepatobiliary cancers, yet the causal relationships remain unclear. Here, we conducted a comprehensive two-sample Mendelian randomization (MR) analysis using genetic instruments from large European cohorts to assess causality among 88 dietary components, 1080 microbiota traits, liver cancer (500 cases, 314,193 controls), and biliary tract cancer (1207 cases, 314,193 controls). We identified significant causal associations of 17 dietary and 101 microbial traits with hepatobiliary cancer risk, while 11 dietary and 70 microbiota traits showed evidence of reverse causality, indicating potential disease-driven alterations. Importantly, a two-step MR mediation analysis revealed that 43 microbial taxa and 6 metabolic pathways significantly mediated dietary influences on hepatobiliary cancer risk; notably, Mollicutes RF9 mediated 31% of the protective effect exerted by zinc on biliary tract cancer. These findings provide genetic evidence delineating gut microbiota as key intermediaries connecting dietary intake to hepatobiliary cancers, highlighting microbiome-targeted dietary strategies as potential preventive interventions. Further research is required to confirm these causal mechanisms and facilitate the development of targeted prevention and therapeutic approaches.},
}

@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics

@article {pmid40613138,
year = {2025},
author = {Filippova, VA and Laptev, GY and Ilina, LA and Yildirim, EA and Ponomareva, ES and Brazhnik, EA and Novikova, NI and Tiurina, DG and Dubrovin, AV and Dubrovina, AS and Sokolova, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN},
title = {Comparative Genomics of Two Novel Bacillus Strains: Microbiomic Insights into the Sequences, Metabolomics, and Potential Safe Use in the Creation of Biopreparations.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {2},
pages = {28227},
doi = {10.31083/FBE28227},
pmid = {40613138},
issn = {1945-0508},
support = {23-16-20007//Russian Science Foundation/ ; 23-16-20007//St. Petersburg Science Foundation/ ; },
mesh = {*Bacillus/genetics/metabolism ; Metabolomics ; *Genomics ; *Genome, Bacterial ; Probiotics ; Bacillus subtilis/genetics/metabolism ; },
abstract = {BACKGROUND: Bacillus bacteria are often used in the production of biopreparations. Moreover, these bacteria can be used in agriculture as probiotics or starters for manufacturing fodder preserved by fermentation (silage). The ability of Bacillus bacteria to produce many biologically active molecules and metabolites with antimicrobial activity means that these bacteria can stimulate plant growth and restore the balance of the microbiome in the digestive system of certain animals.

METHODS: Using molecular biological analysis, bioinformatic annotation, and metabolic profiling of whole genome sequences, we analyzed two promising candidates for creating biopreparations, i.e., two Bacillus strains, namely B. mucilaginosus 159 and B. subtilis 111. We compared the genomes of these two strains and characterized both their microbiomic and metabolomic features.

RESULTS: We demonstrated that both strains lacked elements contributing to the formation of toxic and virulent properties; however, both exhibited potential in the biosynthesis of B vitamins and siderophores. Additionally, these strains could synthesize many antimicrobial substances of different natures and spectrums of action. B. mucilaginosus 159 could synthesize macrolactin H (an antibiotic from the polyketide group), mersacidin (a class II lanthipeptide), and bacilysin. Meanwhile, B. subtilis 111 could synthesize andalusicin (a class III lanthipeptide), bacilysin, macrolactin H, difficidin, bacillaene (a polyene antibiotic), fengycin (a lipopeptide with antifungal activity), and surfactin (another lipopeptide). Further, a unique pathway of intracellular synthesis of the osmoprotectant glycine betaine was identified in B. subtilis 111, with the participation of betaine aldehyde dehydrogenase (BetB); this is not widely represented in bacteria of the genus Bacillus. These compounds can increase osmotic stability, which may be key for manufacturing biological starters for silage preparation.

CONCLUSIONS: These two Bacillus strains are safe for use as probiotic microorganisms or starters in producing preserved fodder. However, B. subtilis 111 may be preferable due to a wider spectrum of synthesized antimicrobial substances and vitamins. Our findings exemplify using genomic technologies to describe the microbiomic and metabolomic characteristics of significant bacterial groups such as Bacillus species.},
}

*Bacillus/genetics/metabolism
Metabolomics
*Genomics
*Genome, Bacterial
Probiotics
Bacillus subtilis/genetics/metabolism

@article {pmid40613137,
year = {2025},
author = {Rajapandi, S and Sukumaran, ES and Prasad, KRN and Venkatesan, AV and Ravichandran, TAS and Sabarathinam, S},
title = {Viral Invasion of the Oral Cavity: A Review of Viral Impact on Oral Health and the Potential Use of Saliva as a Diagnostic Tool.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {2},
pages = {33494},
doi = {10.31083/FBE33494},
pmid = {40613137},
issn = {1945-0508},
mesh = {Humans ; *Saliva/virology ; *Oral Health ; *Mouth/virology ; Microbiota ; *Mouth Diseases/virology/diagnosis ; *Virus Diseases/diagnosis/virology ; },
abstract = {The oral cavity is a complex ecosystem that harbors a diverse microbial community. Viral infections can significantly disrupt this delicate balance, leading to various oral health issues. This review delves into the intricate relationship between viruses and oral health, exploring the impact of both RNA and DNA viruses. We discuss the mechanisms through which these viruses influence the oral microbiome, modulate immune responses, and contribute to various oral diseases, including periodontal disease, oral candidiasis, and oral cancer. Additionally, we highlight the potential of saliva as a valuable diagnostic tool for viral infections and oral health assessment. By understanding the viral-oral health nexus, we can develop effective strategies for prevention, early diagnosis, and targeted interventions to improve oral health outcomes.},
}

Humans
*Saliva/virology
*Oral Health
*Mouth/virology
Microbiota
*Mouth Diseases/virology/diagnosis
*Virus Diseases/diagnosis/virology

@article {pmid40612718,
year = {2025},
author = {Tigran, A and Lusine, H and Ruzanna, H and Inesa, S and Nelli, N and Edita, G and Thomas, H and Inga, B},
title = {Anti-candida activity of Lacticaseibacillus rhamnosus R-2002 and its possible application in candidiasis prevention.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {3},
pages = {441-450},
pmid = {40612718},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Probiotics are used for the treatment of yeast infections, they restore the balance in vaginal microbiome, adhere to epithelial cells, compete against pathogenic bacteria, acidify the environment, produce bacteriocins and modulate the immunity. The aim of the study was to investigate the anti-yeast activity (AYA) of the strain Lacticaseibacillus rhamnosus R-2002 against different Candida species.

MATERIALS AND METHODS: From 20 strains of lactic acid bacteria examined, only L. rhamnosus R-2002 strain demonstrated beneficial properties against yeast. The effects of temperature and pH on AYA and its relation to cell wall were revealed by bi-layer agar assay. The connection of AYA to the cell wall was determined with the sonicated cells.

RESULTS: R-2002 inhibited the growth of C. albicans ATCC 10291, C. tropicalis G 31 and C. albicans G4 (both isolated from vaginal samples). R-2002 maintained its AYA between a wide range of pH and its anti-yeast component/s are extracellular. The tested strain demonstrated stability against the high concentrations of progesterone and metronidazole, making it a suitable candidate for the mitigation of vaginitis.

CONCLUSION: The present study summarizes all the positive features of the strain R-2002 and its potential as a therapeutic agent in the treatment of candidiasis.},
}

@article {pmid40612483,
year = {2025},
author = {Yu, H and Pan, W and Tian, D and Gao, Y},
title = {Deciphering the complexity of enteric niches in Hirschsprung disease: from metaphorical insights to therapeutic transformation.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1579290},
pmid = {40612483},
issn = {2296-2360},
abstract = {Hirschsprung disease (HSCR) is a congenital disorder marked by the absence of ganglion cells in the distal bowel, resulting in severe constipation and bowel obstruction. Surgery is currently the primary treatment for HSCR. However, post-surgical outcomes are unsatisfactory, merely alleviating symptoms of intestinal obstruction. Up to one-third of HSCR patients continue to experience gastrointestinal issues post-surgery, which severely impacts their growth and development and may even threaten their lives. Cell transplantation represents a promising strategy for the radical treatment of HSCR but faces numerous challenges. The mismatch between transplanted cells and the enteric niches is one of the key obstacles in reconstructing the enteric nervous system through cell transplantation. There is an urgent need to "get to the root of the problem" to enhance our understanding of the enteric niches and overcome current limitations. This review synthesizes insights from two metaphorical narratives, "Blind Men and the Elephant" and "Rags To Riches," to provide a comprehensive re-understanding of the enteric niches and their potential for enteric neurogenesis. By examining these narratives, we underscore the importance of the enteric niches in the potential for transformative discoveries in HSCR research.},
}

@article {pmid40612471,
year = {2025},
author = {Arias, RS and Dobbs, JT and Orner, VA and Conforto, EC and Rago, AM and Cazon, LI and Sobolev, VS and Power, IL and Lamb, MC and Massa, AN},
title = {First metagenome- and metatranscriptome dataset of Thecaphora frezzii teliospores, assembly and annotation of a new bacterial genome.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111779},
pmid = {40612471},
issn = {2352-3409},
abstract = {These datasets correspond to sequencing of DNA and RNA extracted from surface-disinfected teliospores of the fungus Thecaphora frezzii Carranza and Lindquist, causal agent of smut disease in peanut (Arachis hypogaea L.). The DNA was sequenced using Pacific Biosciences (PacBio) Sequel II and RNA was sequenced in Illumina MiSeq 300 bp paired end (PE). Initial de novo assembly and Basic Local Alignment Search Tool (BLAST) of contigs to the 16S reference sequence database at NCBI had hits on seven bacterial species: Luteibacter pinisoli, Variovorax paradoxus, Rhizobium metallidurans, Caulobacter segnis, Roseateles violae, Novosphingobium rosa, Herbaspirillum seropedicae, and the fungus T. frezzii. High stringency mapping of the RNA sequences to the genomes of these organisms showed that 96% of the reads corresponded to bacteria and only 4% to T. frezzii. De novo assembly of PacBio reads revealed the whole genome of a Luteibacter sp. with 88.56% or lower similarity to those in NCBI database, whereas most RNA sequences (> 10 million reads) mapped to the new Luteibacter sp. genome assembled here. We annotated the new Luteibacter sp. genome, assessed its completeness by BUSCO, and aligned it to its closest relative, Luteibacter aegosomatissinici. We are not aware of any report that describes bacteria colonizing teliospores of T. frezzii. The DNA and RNA sequencing datasets provided here could be used to study the distribution of prokaryotes colonizing T. frezzii teliospores, and to explore the role of the microbiome of T. frezzii teliospores on the outcome of peanut smut disease.},
}

@article {pmid40612463,
year = {2025},
author = {Heredia, L and Mateo, D and Carrión, N and Torrente, M},
title = {Dataset on neuropsychological profile and microbiota composition in cognitively unimpaired elderly and Alzheimer's patients.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111778},
pmid = {40612463},
issn = {2352-3409},
abstract = {This article presents data collected from a total of 50 older adults (25 healthy controls and 25 diagnosed with Alzheimer's disease). Among the assessments performed in this sample was a comprehensive neurocognitive screening: including working memory, cognitive flexibility, perception, attention, motor coordination, inhibitory control, verbal fluency and visuo-spatial skills. The data presented also include analysis of the participants' gut microbiota using the shot gun approach in faecal samples. Finally, evaluations of the emotional state, level of functioning and adherence to the Mediterranean lifestyle of all participants are also available. Despite the limited sample size due to challenges in patient recruitment, present data could be useful in the identification of microbial signatures potentially predictive of cognitive decline or AD progression and also for helping to the design of clinical trials targeting the microbiome to assess effects on cognitive function. Furthermore, it is well known that the gut microbiota exhibits significant variability associated with lifestyle habits, diet, and geographic location, underscoring the critical influence of environmental and cultural factors in shaping its composition. These data are of utmost importance when considering regional and lifestyle-related diversity in microbiome research, as they can help researchers explore personalized therapeutic approaches and enhance participant stratification in future clinical trials.},
}

@article {pmid40612440,
year = {2025},
author = {Wenjiao, D and Yurou, W and Jiaqi, X and Yan, H and Hongfang, J and Min, C and Jianjin, G},
title = {Animal studies on the modulation of differential efficacy of polyethylene glycol loxenatide by intestinal flora.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1508473},
pmid = {40612440},
issn = {1664-2392},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; *Diabetes Mellitus, Experimental/microbiology/drug therapy/therapy ; *Polyethylene Glycols/pharmacology ; *Diabetes Mellitus, Type 2/microbiology/drug therapy ; *Hypoglycemic Agents/pharmacology/therapeutic use ; Diet, High-Fat/adverse effects ; Blood Glucose ; },
abstract = {BACKGROUND: Gut microbiota has demonstrated an increasingly important role in the onset and development of type 2 diabetes mellitus (T2DM), Further investigations have revealed the interactions between drugs and the gut microbiome. However, there are still gaps in research regarding the potential interactions between the gut microbiota and GLP-1 and their therapeutic response in people with T2DM. In addition, Fecal microbiota transplantation (FMT) has become a promising strategy for patients with T2DM.

50 healthy male C57BL/6 mice were fed a high-fat diet in combination with STZ to establish a T2DM mouse model. 40 mice were divided into the T2DM group (n=10) and the PEX168 group (n=30). the PEX168 group was divided into two subgroups of the IE group (HbA1c ≤6. 5%, n=12) and the SE group (HbA1c >6. 5%, n=12), 12 mice in each group. Using IE mice as fecal donors and SE mice as recipients, fecal microbiota transplantation was performed between the two groups, the FMT group (given fecal bacterial suspension, n=5) and the Sham group (given equal amounts of sterile saline, n=5). The intestinal microorganisms of mice in the IE group (donor) and SE group (recipient) were also analyzed for differences. To assess the protective effect of FMT on drug efficacy and T2DM, and to explore the underlying mechanisms.

RESULTS: After 10 weeks, compared with the control group, the HbA1c of the experimental group was significantly reduced, still, the level of HBA1c of the mice in the unsatisfactory group was significantly higher than that in the ideal group. Compared with the unsatisfactory group, fasting blood glucose, 2h postprandial blood glucose, blood glucose AUC and body weight were significantly reduced in the ideal group. 16srDNA sequencing showed that the levels of Bacteroidota, Akkermansia, Parabacteroides, Bifidobacteria and other bacteria in the ideal efficacy group were significantly higher than those in the non-ideal efficacy group (P<0.05). The levels of Firmicutes, Romboutsia, Clostridium, Turicibacter and other bacteria in the unsatisfactory group were significantly higher than those in the ideal group (P<0.05). The dominant flora of mice in the ideal drug efficacy group was negatively correlated with HbA1c and blood sugar, and the dominant flora of mice in the unsatisfactory drug efficacy group was positively correlated with pro-inflammatory factors such as blood sugar. Moreover, FMT treatment significantly improved the efficacy of PEX168 and liver steatosis in the group with unsatisfactory efficacy.

CONCLUSION: In summary, we used the combined method of 16S rDNA and metabolomics to systematically elucidate the efficacy of microflora on PEX168 and the possible mechanism of FMT in treating T2DM by PEX168. The difference in intestinal flora between individuals can affect the therapeutic effect of drugs. Moreover, FMT therapy can affect multiple metabolic pathways and colonization of beneficial bacteria to maintain the drug's therapeutic effect on T2DM mice.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Male
Mice
Mice, Inbred C57BL
*Fecal Microbiota Transplantation
*Diabetes Mellitus, Experimental/microbiology/drug therapy/therapy
*Polyethylene Glycols/pharmacology
*Diabetes Mellitus, Type 2/microbiology/drug therapy
*Hypoglycemic Agents/pharmacology/therapeutic use
Diet, High-Fat/adverse effects
Blood Glucose

@article {pmid40612394,
year = {2025},
author = {Ma, X and Zhang, H},
title = {Meta-analysis of probiotics metabolites in gastrointestinal tract and metabolic health.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619501},
pmid = {40612394},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/metabolism ; *Gastrointestinal Tract/metabolism/microbiology ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Gene Expression Profiling ; },
abstract = {INTRODUCTION: The gastrointestinal (GI) tract acts as an essential interface between the host and the microbiota, with microbial metabolites exerting a significant role in regulating host physiology.

METHODS: Integrative network-based methodology that combines metabolite-protein interactions with tissue-specific transcriptomics to uncover host targets of probiotic-derived metabolites and determine their potential biological significance. Utilizing curated interaction data, it is about to construct metabolite-host protein network and prioritised genes using centrality metrics. Gene expression analysis across human tissues indicated that some high-degree genes, including SLC27A4, LCN12, and APOD, are abundant in GI areas including small intestine, colon, and duodenum, indicating a potential role in local host-microbe interactions. Further metabolite-specific expression analysis revealed separate but overlapping expression landscapes. 10-hydroxy-cis-12-octadecenoic acid has been associated to increased production of sialyltransferases and neuraminidase in metabolically and immunologically active tissues.

RESULTS AND DISCUSSION: Glycodeoxycholic acid was associated with high levels of lipocalins and fatty acid transporters in enterohepatic tissues, indicating functions in bile acid metabolism and lipid transport. Meanwhile, N-(1-carbamoyl-2-phenyl-ethyl) butyramide was linked to detoxifying enzymes that are highly expressed in the liver, kidney, and gastrointestinal tissues. Collectively, these data reveal a tissue-specific molecular architecture that governs host responses to microbial metabolites, notably in the GI tract. Our findings shed light on how microbial compounds interact with host pathways at both the local and systemic levels, paving the way for new microbiome-targeted treatments and precision feeding initiatives.},
}

Humans
*Probiotics/metabolism
*Gastrointestinal Tract/metabolism/microbiology
*Gastrointestinal Microbiome
Host Microbial Interactions
Gene Expression Profiling

@article {pmid40612314,
year = {2025},
author = {Sequeira-Bisson, IR and Fraser, K and Leiu, KH and Penhaligan, J and Joblin-Mills, A and Plank, LD and Murphy, R and Taylor, MW and Gasser, O and Conroy, DM and Jiang, Y and Lu, LWW and Poppitt, SD and Miles-Chan, JL},
title = {Design and conduct of a full diet-controlled, parallel, 2-week residential trial for diabetes prevention without weight loss in Asian Chinese and European Caucasian adults with prediabetes: the New Zealand SYNERGY study.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590579},
pmid = {40612314},
issn = {2296-861X},
abstract = {BACKGROUND: The causal underpinning of increased metabolic risk and previously observed dichotomous plasma metabolome in Asian Chinese vs. European Caucasian remains undetermined and may be hypothesised as attributed to ethnicity (genetic background), pathology (dysglycaemia) and/or lifestyle (habitual diet). We aimed to investigate the underlying cause(s) and the effect of dietary intervention on biomarkers of type 2 diabetes (T2D) in cohorts with prediabetes. The diets are a generic current Best Practice Healthy Diet ('BPHD'), and a New Zealand-specific healthy diet ('SYNERGY') based on the Mediterranean Diet. We hypothesise, firstly, that 14-days of matched BPHD in Asian Chinese vs. European Caucasian cohorts (ethnicity; within-diet comparison) will attenuate the previously observed dichotomy in plasma metabolome. Secondly, that both diets will improve risk markers over 14 days vs. baseline, with significant improvement with SYNERGY compared to BPHD in Asian Chinese cohorts (diet; within-ethnicity comparison).

METHODS: We conducted a 2-week, fully diet-controlled, residential trial in 20 Asian Chinese (n = 10 per diet group) and 10 European Caucasian (BPHD only) adults with prediabetes. Participants were phenotyped (dual-energy X-ray absorptiometry, magnetic resonance imaging/spectroscopy) prior to the intervention. On Day 1 (D1) and D15 assessments included anthropometry, collection of urine, faecal (microbiome analysis) and fasted blood samples, conduct of 2-h oral glucose tolerance test (established clinical, metabolome, immune markers) and indirect calorimetry (resting metabolic rate, postprandial glucose-induced thermogenesis). Additional fasted urine and blood samples were collected on D2, D7 (mid-way) and D14, with a focus group/interview on the evening of D7. Meals and snacks were calculated based on individual energy requirements for body weight maintenance, dietary compliance was supervised, and body weight monitored daily.

DISCUSSION: This study aims to identify ethnic-specific dietary responses in a fully-controlled residential setting; to determine cause/s of the dichotomous plasma metabolome between the two ethnic groups; also to validate these biomarkers as sensitive to dietary intervention using a 'whole of diet' approach. Specifically, to determine the efficacy of BPHD and SYNERGY for T2D risk amelioration in the absence of body weight loss. Findings will inform design of larger 'free-living' community interventions and explore the feasibility of use of these diets within the community.

The study was prospectively registered on 22 March 2021 with the Australian New Zealand Clinical Trials Registry ACTRN12621000318886.},
}

@article {pmid40612273,
year = {2025},
author = {Constantino-Jonapa, LA and Aguilar-Villegas, OR and Hernández-Ruiz, P and Escalona-Montaño, AR and Pallecchi, M and González-Pacheco, H and Bartolucci, G and Baldi, S and Amezcua-Guerra, LM and Amedei, A and Aguirre-García, MM},
title = {The link between inflammatory/ SCFA profiles and oral/gut microbiome: an observational study in patients with ST-segment elevation myocardial infarction.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100423},
pmid = {40612273},
issn = {2666-5174},
abstract = {Acute myocardial infarction (AMI) is a leading cause of mortality in Mexico. The microbiota plays a crucial role in immune regulation, and its dysbiosis promotes low-grade inflammation, a key contributor to AMI development. This study aimed to compare the oral (OM) and gut microbiota (GM) composition in patients with ST-segment elevation myocardial infarction (STEMI) and healthy controls. Additionally, we explored the interaction between these microbiomes and their correlations with inflammatory profiles and metabolites. In this study, we included 36 STEMI patients and 12 healthy subjects. The composition of both GM and OM was analyzed through 16S sequencing of dental plaque and stool samples. Short-chain fatty acids (SCFAs) were measured via gas chromatography-mass spectrometry, while serum cytokines were assessed using flow cytometry. STEMI patients exhibited significant differences in OM alpha and beta diversity, while GM structure remained unchanged compared to healthy group. Several differentially abundant genera were identified in both OM and GM. Regarding SCFA profiles, Healthy subjects displayed a higher abundance of isovaleric acid, whereas isobutyric and 2-methylbutyric acids were significantly higher in STEMI patients. Moreover, correlations between circulating SCFAs, cytokines, and microbiota composition were observed in both niches. Furthermore, network analysis suggests that oral bacteria, particularly those linked to periodontal disease, can potentially influence GM by interacting with SCFA-producing bacteria. This is the first study in México to comprehensively explore OM and GM in STEMI patients. Our findings highlight the potential for developing preventive strategies against myocardial infarction by exploring both oral and gut microbiomes, as well inflammatory markers and SCFAs.},
}

@article {pmid40612152,
year = {2025},
author = {Bonde, CS and Drøhse, FB and Büdeyri Gökgöz, N and Krych, L and Nielsen, DS and Petersen, HH and Matthiesen, R and Pedersen, NR and Geldhof, P and Williams, AR and Thamsborg, SM and Mejer, H},
title = {Dietary supplementation with fermented rapeseed and seaweed modulates parasite infections and gut microbiota in outdoor pigs.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1565686},
pmid = {40612152},
issn = {2297-1769},
abstract = {Outdoor pig production systems can increase exposure to helminth infections such as Ascaris suum. Anthelmintic drug treatments are currently the primary strategy for controlling such infections; however, this approach is considered unsustainable due to the risk of parasites developing anthelmintic resistance. This study investigated the potential anthelmintic effect of a 2% w/w fermented rapeseed-seaweed (FRS) dietary supplement administered over an 11-12 week period in growing-finisher pigs. Outcomes assessed included parasitic fecal egg counts (FEC), serology, gut microbiota composition, and systemic inflammation. The FRS supplement consisted of 6% Saccharina latissima, 6% Ascophyllum nodosum, and 88% rapeseed meal (based on dry matter) and was provided in two different batches. Supplementation with FRS tended to lower FEC and reduce the incidence of A. suum infection. However, this effect varied between batches. FRS also influenced gut microbiota composition: pigs that were fed the second batch of FRS showed an increased relative abundance of several Bacteroidetes members (e.g., Prevotella), while unsupplemented pigs were enriched with various taxa from the Firmicutes phylum, such as Clostridium spp. Furthermore, pigs fed the second batch of FTR showed reduced daily weight gain compared to those fed the control diet. Overall, our results indicate that FRS modulates the gut microbiota toward a composition potentially associated with improved gut health and may have promise as a prebiotic or novel feed additive to help reduce helminth infections.},
}

@article {pmid40611979,
year = {2025},
author = {Setubal, JC and Paccanaro, A},
title = {Editorial: Expert opinions in genomic analysis.},
journal = {Frontiers in bioinformatics},
volume = {5},
number = {},
pages = {1641083},
doi = {10.3389/fbinf.2025.1641083},
pmid = {40611979},
issn = {2673-7647},
}

@article {pmid40611965,
year = {2025},
author = {Ivanova, M and Aarestrup, FM and Otani, S},
title = {Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597804},
pmid = {40611965},
issn = {1664-302X},
abstract = {The effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical importance for surveillance applications. Here, we evaluate how different multiplexing levels (four and eight samples per flowcell) on two ONT platforms, GridION and PromethION, influence the detection of ARGs, bacterial taxa and pathogens. While overall resistome and bacterial community profiles remained comparable across multiplexing levels, ARG detection was more comprehensive in the four-plex setting with low-abundance genes. Similarly, pathogen detection was more sensitive in the four-plex, identifying a broader range of low abundant bacterial taxa compared to the eight-plex. However, triplicate sequencing of the same microbiomes revealed that these differences were primarily due to sequencing variability rather than multiplexing itself, as similar inconsistencies were observed across replicates. Given that eight-plex sequencing is more cost-effective while still capturing the overall resistome and bacterial community composition, it may be the preferred option for general surveillance. Lower multiplexing levels may be advantageous for applications requiring enhanced sensitivity, such as detailed pathogen research. These findings highlight the trade-off between multiplexing efficiency, sequencing depth, and cost in metagenomic studies.},
}

@article {pmid40611952,
year = {2025},
author = {Malal, H and Garcia, JA and Marrs, A and Ait Hamza, M and Emerson, C and Nocco, M and Lakhtar, H and Lazcano, C},
title = {Organic and inorganic fertilizers modulate the response of the soil microbiome to salinity stress.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1551586},
pmid = {40611952},
issn = {1664-302X},
abstract = {Salinity stress threatens soil microbiomes, a key driver of soil multifunctionality and health. This study employed high-throughput sequencing of 16S rRNA, PLFAs, multifunctionality index, and co-occurrence networks to gain a comprehensive understanding of the dynamic responses of soil microbiomes to salinity stress gradient (0, 0.4 and 1 mol NaCl). Additionally, we investigated how these responses are shaped by the addition of vermicompost and NPK fertilizer during short-term (2-h) and long-term (70-day) incubation periods. Salinity stress reduced bacterial and fungal phospholipid fatty acids (PLFA) concentrations in the short-term. Over the long-term, the microbial community evolved into a new pattern under salt stress, favoring the presence of Bacteriodota, a salt-tolerant phylum, while decreasing the relative abundance of Acidobacteriota and Planctomycetota, which are more salt-sensitive. Furthermore, salinity decreased species richness by 11.33% and soil multifunctionality by 21.48% but increased microbial network complexity while decreasing its stability. Incorporating vermicompost increased bacterial and fungal PLFAs, enhanced bacterial diversity by 2.33%, promoted salt-tolerant bacteria, and increased the complexity and stability of the bacterial network. Conversely, the application of NPK fertilizer reduced bacterial richness, alpha diversity and soil multifunctionality by 14.52, 5.83, and 12.34%, respectively, further disrupting the microbial community and making resilience to salinity stress more challenging. Furthermore, NPK fertilization increased bacterial network complexity but decreased its stability. This study underscores the significance of employing vermicompost to improve the health of saline soils. Furthermore, it emphasizes the negative impacts of NPK fertilizer on soil microbial structure and function and hinder its recovery from salinity's impacts.},
}

@article {pmid40611941,
year = {2025},
author = {Ramírez-Fernández, L and Saldarriaga-Córdoba, M and Silva, AX and Napolitano, C and Rodríguez-San Pedro, A},
title = {Eukaryotic gut community of the bat Myotis arescens in anthropized landscapes in Chile.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19563},
pmid = {40611941},
issn = {2167-8359},
mesh = {*Chiroptera/microbiology/parasitology ; Chile ; Animals ; Ecosystem ; Feces/parasitology/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Eukaryota/isolation & purification/genetics ; },
abstract = {BACKGROUND: Human-driven environmental changes can disrupt wildlife habitats, forcing animals to adapt to fragmented or degraded ecosystems. In some cases, this leads to increased proximity between wildlife and human populations, heightening the risk of pathogen spillover. Bats, as key ecological players, are particularly sensitive to such disturbances. While some species decline in heavily altered environments, others adapt and thrive near human settlements, increasing the likelihood of encounters. Given that bats can host a wide range of zoonotic pathogens, this adaptive behavior raises important public health concerns. Despite their ecological significance and their role in zoonotic disease dynamics, the gut eukaryotes communities associated with bats remain less studied.

METHODS: This study focused on the Valparaíso Myotis (Myotis arescens), an insectivorous bat species endemic to central Chile that is significantly impacted by anthropogenic deforestation and habitat fragmentation. We characterized the gut eukaryotic communities of M. arescens through fecal sample analysis. Targeted microbial groups included fungi, metazoan parasites, and protists. High-throughput sequencing was employed to assess gut eukaryotes diversity, and beta diversity analysis was conducted to explore clustering patterns in relation to environmental variables, such as vegetation cover and land use types.

RESULTS: Our analyses revealed that the gut eukaryotic community of M. arescens consistently included taxa from the Apicomplexa, Ascomycota, and Basidiomycota phyla, with Apicomplexa being the most abundant. Beta diversity analysis showed distinct clustering by sampling location, with the percentage of native vegetation identified as the primary factor shaping gut eukaryotic community structure. Other influential variables included the presence of annual crops, orchards, water bodies, and urban areas. Notably, a high abundance of Apicomplexa-particularly amplicon sequence variants (ASVs) related to the genus Eimeria-was detected in bat feces across sites with varying degrees of anthropogenic disturbance.

CONCLUSIONS: This study highlights the significant role of native vegetation in shaping the eukaryotic gut community of M. arescens, suggesting that gut eukaryotic composition can serve as a bioindicator of bat health and habitat quality. Among the dominant taxa, members of the genus Eimeria were frequently detected across sites with varying degrees of anthropogenic disturbance. Although Eimeria is generally considered host-specific and not zoonotic, its high prevalence in bat gut communities points to the need for further research into its ecological role and potential implications for wildlife health. Overall, these findings underscore the importance of conserving native habitats to maintain ecosystem integrity and support healthy bat populations.},
}

*Chiroptera/microbiology/parasitology
Chile
Animals
Ecosystem
Feces/parasitology/microbiology
*Gastrointestinal Microbiome
Humans
*Eukaryota/isolation & purification/genetics

@article {pmid40611932,
year = {2025},
author = {Yinadsawaphan, T and Kulthamrongsri, N and Malone, RM and Surapongpairat, S and Puchongmart, C and Thiravetyan, B and Imwattana, K and Na Witayanan, J},
title = {A rare case of native mitral valve infective endocarditis by Lactobacillus jensenii in a healthy young patient.},
journal = {IJID regions},
volume = {15},
number = {},
pages = {100648},
pmid = {40611932},
issn = {2772-7076},
abstract = {Lactobacillus jensenii, a Gram-positive facultative anaerobic bacterium, is part of the normal vaginal microbiome and is occasionally found in fermented foods and probiotics. It is a rare cause of infections, with infective endocarditis (IE) being exceedingly uncommon. We report a case of IE caused by Lactobacillus jensenii in a previously healthy 15-year-old female who presented with progressive dyspnea, fever, and severe mitral regurgitation. Echocardiography revealed a vegetative mass on the anterior mitral leaflet. Blood cultures identified L. jensenii using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry. Surgical repair confirmed myxomatous degeneration and chronic inflammation of the mitral valve. The patient fully recovered after surgery and a 6-week antibiotic course. A review of 12 reported cases of L. jensenii IE, including our case, shows a predominance in immunocompetent females, possibly due to its role as a vaginal commensal. Most cases involved native valves with underlying pathology facilitating bacterial colonization. An empirical regimen with ampicillin and gentamicin is effective against L. jensenii. A treatment duration of 4-6 weeks is sufficient, with favorable outcomes.},
}

@article {pmid40611420,
year = {2025},
author = {Rezaei, M and Jalali, A and Sadah Al-Azzawi, DH},
title = {Engineered Bacteriophages: Advances in Phage Genome Redesign Strategies for Therapeutic and Environmental Applications.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665372719250616085616},
pmid = {40611420},
issn = {1875-5305},
abstract = {Bacteriophages, or phages, have emerged as powerful platforms in synthetic biology, offering innovative solutions for therapeutic and environmental challenges through advanced genome redesign strategies. This review explores a wide range of phage engineering techniques, including CRISPR (clustered regularly-interspaced short palindromic repeats)-Cas systems, phage display, random and site-directed mutagenesis, retrons, and rebooting approaches, highlighting their potential to create phages with tailored functionalities. CRISPR-Cas systems enable precise genome editing, allowing the development of phages with expanded host ranges, biofilm degradation capabilities, and targeted antimicrobial activity. Phage display facilitates the presentation of peptides on phage surfaces, enabling applications in targeted drug delivery, tumor imaging, and bioremediation. Beyond these, techniques like retron-mediated recombination and homologous recombination offer additional avenues for precise phage genome modification. In the therapeutic realm, engineered phages show promise in combating drug-resistant infections, modulating the microbiome, and delivering targeted therapies for cancer and other diseases. Environmentally, phage-based strategies, such as the use of phage-displayed metal-binding peptides, provide innovative solutions for bioremediation and reducing exposure to toxic heavy metals. This review also addresses challenges, such as phage resistance, immune responses, and the limitations of current engineering methods, while exploring future directions, including the development of improved CRISPR systems, phage-based biosensors, and high-throughput screening platforms. By integrating cutting-edge genome redesign strategies with diverse applications, this review underscores the transformative potential of engineered bacteriophages in addressing global healthcare and environmental sustainability challenges.},
}

@article {pmid40611411,
year = {2025},
author = {Islam, A},
title = {Advances in Microbiome Research: Implications for Infectious Disease Management and Treatment.},
journal = {Recent advances in anti-infective drug discovery},
volume = {},
number = {},
pages = {},
doi = {10.2174/0127724344384934250624040634},
pmid = {40611411},
issn = {2772-4352},
abstract = {INTRODUCTION: The human microbiome plays a pivotal role in health and disease, with microbial imbalances (dysbiosis) increasingly linked to heightened susceptibility to infections and exacerbated disease severity. This review explores how the microbiome confers protection through mechanisms, such as colonization resistance, immune modulation, and antimicrobial metabolite production, while also examining its potential as a predictive tool for infection risk and outcomes, as exemplified in COVID-19.

METHODS: This article synthesizes current literature on microbiome dynamics, leveraging advances in high-throughput sequencing, bioinformatics, and machine learning to analyze microbial profiles and identify biomarkers. It evaluates microbiome-based therapeutic strategies, including probiotics, prebiotics, and engineered microbes, and assesses challenges in translating these approaches into clinical practice.

RESULTS: Microbiome profiles demonstrate prognostic value in predicting infection risk and severity, supported by enhanced analytical tools that enable precise biomarker discovery for diagnostics and personalized medicine. Therapeutic interventions show promise in restoring microbial balance and combating infections, though clinical adoption is hindered by variability, regulatory hurdles, and the need for standardized methodologies.

CONCLUSION: Integrating microbiome insights into clinical practice requires rigorous clinical trials, standardized protocols, and resolution of ethical and regulatory challenges. Future research should focus on elucidating microbiome-host-pathogen interactions and developing targeted interventions, and advanced computational models are critical to unlocking the full potential of microbiome-based diagnostics and therapeutics for infectious disease management.},
}

@article {pmid40611327,
year = {2025},
author = {Bustos, IG and Serrano-Mayorga, CC and Guerrero, JL and Baker, JM and Brown, C and Falkowski, N and Ranjan, P and Acosta-Gonzalez, A and Mendez, LM and Garcia-Cordoba, A and Echeverry-Gutierrez, A and Bojaca, DA and Chisica-Mahecha, M and Guarin-Tequia, N and Romero-Romero, L and Gonzalez-Juarbe, N and Rodriguez, A and Cala, MP and Martin-Loeches, I and Chotirmall, SH and Dickson, RP and Reyes, LF},
title = {Longitudinal analysis of lung microbiome, immune response, and metabolism in ventilator-associated pneumonia: a cohort study.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {275},
pmid = {40611327},
issn = {1466-609X},
support = {MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; MED-260-2019//Universidad de La Sabana , Colombia/ ; },
mesh = {Humans ; *Pneumonia, Ventilator-Associated/physiopathology/microbiology/immunology/metabolism ; Male ; Female ; Middle Aged ; *Microbiota/physiology ; Cohort Studies ; Aged ; *Lung/microbiology/physiopathology/metabolism ; Longitudinal Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Respiration, Artificial/adverse effects ; Cytokines/analysis ; },
abstract = {RATIONALE: Ventilator-associated pneumonia (VAP) is a common complication in patients under invasive mechanical ventilation (IMV), yet its underlying mechanisms remain poorly understood. This study investigated the lung microbiome, inflammatory response, and metabolism in patients undergoing IMV to identify factors that may predispose them to developing VAP.

OBJECTIVES: To investigate how changes in lung microbiome composition, inflammatory response, and metabolic profiles may predispose patients undergoing IMV to develop VAP.

METHODS: Patients requiring IMV for at least 48 h due to non-infectious respiratory failure were enrolled. Bronchoalveolar lavage (BAL) samples were collected at baseline, upon VAP diagnosis, or after 72 h for non-VAP cases. DNA sequencing, cytokine quantification, and metabolomic analyses were performed.

RESULTS: Of the 80 patients, 41 (51%) developed VAP. No significant differences in alpha or beta diversity of the lung microbiome were observed between groups. However, both groups showed changes in microbiome composition over time, suggesting an impact of IMV. Tumour necrosis factor-alpha (TNF-α) lung levels were significantly higher in VAP patients, while lung interleukin-1 beta (IL-1β) increased in all patients. Metabolomic analysis revealed shifts in pentose phosphate and citric acid cycle pathways, indicating a transition to anaerobic metabolism in the lungs of VAP patients.

CONCLUSIONS: Mechanical ventilation was associated with temporal changes in lung microbiome composition independent of VAP development. VAP cases exhibited higher TNF-α levels and metabolic profiles indicative of anaerobic adaptation, while IL-1β elevations were primarily linked to mechanical ventilation rather than infection.},
}

Humans
*Pneumonia, Ventilator-Associated/physiopathology/microbiology/immunology/metabolism
Male
Female
Middle Aged
*Microbiota/physiology
Cohort Studies
Aged
*Lung/microbiology/physiopathology/metabolism
Longitudinal Studies
Bronchoalveolar Lavage Fluid/microbiology
Respiration, Artificial/adverse effects
Cytokines/analysis

@article {pmid40611207,
year = {2025},
author = {Wang, Q and Zhang, M and Meng, M and Luo, Z and Pan, Z and Deng, L and Qin, J and Guo, B and Zhu, D and Zhang, Y and Guo, H and Liang, Y and Su, Z},
title = {Integration bile acid metabolomics and gut microbiome to study the anti-liver fibrosis effects of total alkaloids of Corydalis saxicola Bunting.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {106},
pmid = {40611207},
issn = {1749-8546},
support = {82060763//National Natural Science Foundation of China/ ; GXFCDP-PS-2022//Guangxi First-class Discipline Project for Pharmaceutical Sciences/ ; GXQH202409//Guangxi Youth Qihuang Scholars Training Project/ ; },
abstract = {BACKGROUND: Bile acids and gut microbiota participate in the pathogenesis of liver fibrosis (LF). The total alkaloids of Corydalis saxicola Bunting (TACS) is a traditional Chinese medicine extract that has been used to treat LF, but the underlying mechanisms are not clear. This study performed integrated metabolomics and gut microbiome analysis to study the anti-LF mechanism of TACS using a rat model.

METHODS: Ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) was used to identify the chemical compounds in TACS. Biochemical and histopathological analysis were performed to determine the efficacy of TACS. Bile acid-targeted metabolomics was used to assess changes in the bile acid (BA) profiles in TACS-treated LF rats. 16S rRNA gene sequencing and metagenomics were used to assess changes in the gut microbiota of the TACS-treated LF rats. Antibiotic cocktail treatment and fecal microbiota transplantation (FMT) were used to determine the relationship between the gut microbiota and the anti-LF effects of TACS. Metagenomics was used to identify significantly enriched gut microbiota after TACS treatment and its correlation with the anti-LF effects was verified by in vivo experiments.

RESULTS: TACS treatment significantly reduced the levels of serum liver enzymes, fibrosis and pro-inflammatory cytokines in the liver. TACS significantly increased the levels of chenodeoxycholic acid (CDCA) and taurochenodeoxycholic acid (TCDCA) in the cecum and decreased the levels of cholic acid (CA) and deoxycholic acid (DCA) in the liver of the LF rats. TACS significantly increased the abundances of Lactobacillus and Akkermansia in the LF rats. Antibiotic cocktail treatment and FMT have shown that the effect of TACS cure liver fibrosis depends on the gut microbiota. The abundance of Lactobacillus reuteri was significantly increased by TACS. Administration of Lactobacillus reuteri via gavage ameliorated LF.

CONCLUSIONS: TACS exerted anti-LF effects in rats by modulating bile acid metabolism and gut microbiome.},
}

@article {pmid40610607,
year = {2025},
author = {Jurvansuu, J and Länsivaara, A and Palmroth, M and Kaarela, O and Hyöty, H and Oikarinen, S and Lehto, KM},
title = {Machine learning-based identification of wastewater treatment plant-specific microbial indicators using 16S rRNA gene sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23771},
pmid = {40610607},
issn = {2045-2322},
support = {Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; Tampere3 Innovation Competition (2017 - 2018)//City of Tampere, Finland/ ; },
mesh = {*Machine Learning ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Finland ; Water Purification ; },
abstract = {Effluent released from municipal wastewater treatment plants reflects the microbial communities responsible for degrading and removing contaminants within the plants. Monitoring this effluent offers essential insights into its environmental impacts, the efficiency of treatment processes, and the presence of emerging contaminants. To support improved monitoring and source attribution, our study employed a machine-learning framework to identify microbial indicators capable of distinguishing between municipal treatment plants based on effluent microbiota. We collected 57 effluent samples for sequencing of the V4 region of the 16S rRNA gene from six treatment plants in the Pirkanmaa region in Finland between 2016 and 2018. Characterising the microbiome revealed that although each plant had unique microbial profiles, their overall diversity and richness were similar. This provided a robust foundation for identifying plant-specific microbes. Using ANOVA-F for feature selection, we focused on the genus level due to its informative prevalence. Among various models tested, the Gaussian Naive Bayes model yielded the highest accuracy with the fewest relevant microbes. We identified nine bacterial genera and one archaeon, whose relative abundances predicted the origin of the effluent with 92% accuracy. Our study outlines a framework for the cost-effective and rapid identification of the origin of effluent or changes in the treatment process, demonstrating the power of machine learning in environmental monitoring and management.},
}

*Machine Learning
*Wastewater/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Microbiota/genetics
Finland
Water Purification

@article {pmid40610597,
year = {2025},
author = {Willyard, C},
title = {Home medical tests miss the mark.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40610597},
issn = {1476-4687},
}

@article {pmid40610473,
year = {2025},
author = {Ivanova, EA and Suleymanov, AR and Nikitin, DA and Semenov, MV and Abakumov, EV},
title = {Machine learning-based mapping of Acidobacteriota and Planctomycetota using 16 S rRNA gene metabarcoding data across soils in Russia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23763},
pmid = {40610473},
issn = {2045-2322},
support = {24-44-00006//Russian Science Support Foundation/ ; 24-44-00006//Russian Science Support Foundation/ ; },
mesh = {*Machine Learning ; *Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; Russia ; *DNA Barcoding, Taxonomic/methods ; Soil/chemistry ; Microbiota/genetics ; *Acidobacteria/genetics/classification ; Ecosystem ; },
abstract = {The soil microbiome plays a crucial role in maintaining healthy ecosystems and supporting sustainable agriculture. Studying its biogeographical structure and distribution is essential for understanding the rates and mechanisms of microbially mediated soil ecosystem services. This study aimed to investigate the spatial distribution patterns of Acidobacteriota and Planctomycetota across soils in Russia, summarizing data from 16S rRNA gene metabarcoding of topsoils. A machine learning approach (Random Forest) was employed to generate digital distribution maps using climatic, topographic, vegetation, geological, and soil variables. Model interpration was performed using variable importance assessment and Shapley values. According to the error metrics, the Acidobacteriota model achieved a root mean squared error (RMSE) of 6.67% and an R[2] of 0.41, while the Planctomycetota model achieved an RMSE of 2.04% and an R[2] of 0.46. Both phyla exhibited similar spatial distribution patterns, with relative abundance decreasing from North to South. For Acidobacteriota, vegetation cover, surface temperature, and soil pH were significant predictors, whereas the relative abundance of Planctomycetota was mainly influenced by climatic variables. Specifically, Acidobacteriota were more abundant in areas with dense vegetation, stable surface temperatures, and acidic soils. In contrast, Planctomycetota showed reduced abundance in regions with higher levels of precipitable water vapor. These results highlight the potential of machine learning techniques to visualize predictive biogeographic patterns in soil microbial taxa abundance at the phylum level. Despite limitations related to the heterogeneous nature of source data, focusing on higher taxonomic ranks less sensitive to methodological variation enabled to identify preliminary large-scale distribution trends of microbial phyla in soils.},
}

*Machine Learning
*Soil Microbiology
*RNA, Ribosomal, 16S/genetics
Russia
*DNA Barcoding, Taxonomic/methods
Soil/chemistry
Microbiota/genetics
*Acidobacteria/genetics/classification
Ecosystem

@article {pmid40610420,
year = {2025},
author = {Knodel, S and Main, L and DeLeon, M and Lamont, A and Edward, J and Gupta, AK and Noel-Romas, L and Mohammed, S and Tattersall, T and Wong, J and Hull, M and Grennan, T and Burgener, AD},
title = {Impact of doxycycline pre-exposure prophylaxis (doxyPrEP) for sexually transmitted infections on the microbiome of men who have sex with men on HIV PrEP.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6143},
pmid = {40610420},
issn = {2041-1723},
support = {365358//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; HB3-164066//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; 2P30 AI036219-26A, 5P30DA054557//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; IN-CA-276-4012//Gilead Sciences (Gilead)/ ; },
mesh = {Humans ; Male ; *Doxycycline/therapeutic use/administration & dosage/pharmacology ; *Pre-Exposure Prophylaxis/methods ; Adult ; Homosexuality, Male ; *HIV Infections/prevention & control ; Pilot Projects ; *Microbiota/drug effects ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Middle Aged ; *Sexually Transmitted Diseases/prevention & control/microbiology/drug therapy ; RNA, Ribosomal, 16S/genetics ; Rectum/microbiology ; Emtricitabine/therapeutic use ; Sexual and Gender Minorities ; },
abstract = {Doxycycline pre-exposure prophylaxis (doxyPrEP) has shown potential in preventing bacterial sexually transmitted infections, but the impact on the microbiome is unknown. This study assessed rectal microbiome changes over 48 weeks in 41 participants on HIV PrEP (tenofovir disoproxil fumarate/emtricitabine) enrolled in an open-label, randomized pilot trial comparing immediate (100 mg PO daily started immediately and continued to week 48) versus deferred doxyPrEP (100 mg PO daily starting at week 24, continued to week 48) in HIV-negative gay and bisexual men (Clinical Trial #: NCT02844634). Primary study outcomes included feasibility, adherence, and tolerability of the dual PrEP regimen, while exploratory outcomes included rectal microbiome changes. We performed 16S rRNA sequencing from participants that collected baseline, week 24, and week 48 samples. Microbial composition did not significantly change over time in either study arm as measured by individual taxa levels, or alpha and beta diversity at the genus level. A slight decrease (< 10%) in alpha diversity was observed at the phylum level in the immediate arm, but not the deferred arm. This study shows doxyPrEP use results in minimal compositional changes in the microbiome over 12 months. Further research is needed to explore the impact of doxycycline for STI prevention on microbiome function and antimicrobial resistance.},
}

Humans
Male
*Doxycycline/therapeutic use/administration & dosage/pharmacology
*Pre-Exposure Prophylaxis/methods
Adult
Homosexuality, Male
*HIV Infections/prevention & control
Pilot Projects
*Microbiota/drug effects
*Anti-Bacterial Agents/therapeutic use/administration & dosage
Middle Aged
*Sexually Transmitted Diseases/prevention & control/microbiology/drug therapy
RNA, Ribosomal, 16S/genetics
Rectum/microbiology
Emtricitabine/therapeutic use
Sexual and Gender Minorities

@article {pmid40609987,
year = {2025},
author = {Chen, CC and Lin, TY and Wu, WK and Panyod, S and Lin, YK and Lin, YH and Chan, ST and Wu, MS and Lee, CN and Chiang, CF},
title = {Gut-breast axis modulation through Streptococcus thermophilus TCI633 supplementation: a study on mother-infant microbiome dynamics.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-8},
doi = {10.1163/18762891-bja00082},
pmid = {40609987},
issn = {1876-2891},
abstract = {Breast milk provides essential nutrition and bioactive components, including probiotics, which contribute to the development of a balanced infant microbiota and a strengthened immune system. The gut-breast axis theory suggests that the maternal gut microbiota may influence the microbiota and composition of breast milk through immune-mediated signaling. This study aimed to investigate the colonization potential of S. thermophilus TCI633 in the infant gut and to explore its possible transfer via the gut-breast axis. A total of 30 exclusively breastfeeding mother-infant pairs were recruited. Mothers took TCI633 daily for one month following hospital discharge. Breast milk, maternal feces, and infant fecal samples were collected and analyzed for microbiota composition, S. thermophilus abundance, and detection of TCI633-specific gene fragments. Results showed minor changes in the microbiota composition of breast milk and fecal samples in the TCI633 group, with a slight increase in S. thermophilus abundance. Furthermore, TCI633-specific gene fragments were detected in 66.7% of infant fecal samples, suggesting potential microbial transfer and colonisation. These findings provide preliminary evidence supporting the feasibility of TCI633 transmission via the gut-breast axis, although further research is needed to determine its functional significance.},
}

@article {pmid40609897,
year = {2025},
author = {Elhag, MRA and Abu-Median, AB and Da Boit, M and Haris, PI and Madkour, MI and Alkawamleh, DH and Faris, M},
title = {Transforming Gut Health through Ramadan Intermittent Fasting: A Review on Metabolic and Microbiomic Insights.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.06.051},
pmid = {40609897},
issn = {2405-4577},
abstract = {The gut microbiome's crucial role in health and disease has spurred interest in dietary interventions to modulate its composition and enhance microbial diversity. While approaches to optimize the microbiome exist, universal guidelines remain elusive due to the complexity of the ecosystem and interindividual variability. This review examines the biochemical changes associated with intermittent fasting (IF), specifically Ramadan intermittent fasting (RIF), which involves complete abstinence from food and fluids during daylight hours. Unlike other IF protocols, RIF's complete fasting presents a unique opportunity to investigate its specific effects on the gut microbiome and metabolic pathways. Preliminary studies suggest that RIF favorably modulates microbial profiles, potentially increasing beneficial taxa such as Akkermansia muciniphila and Bacteroides fragilis. However, limitations such as small sample sizes and heterogeneous study designs necessitate further research to fully elucidate the microbiome-driven mechanisms underlying IF's potential health benefits, particularly in relation to cancer, diabetes, and neurodegenerative diseases. Variations in key taxa, such as Dorea, Klebsiella, and Faecalibacterium, influenced by demographics, further emphasize this need. The RIF model possesses unique mechanisms among IF and holds promise for future applications.},
}

@article {pmid40609837,
year = {2025},
author = {Dubé-Zinatelli, E and Anderson, F and Ismail, N},
title = {The overlooked mental health burden of polycystic ovary syndrome: neurobiological insights into PCOS-related depression.},
journal = {Frontiers in neuroendocrinology},
volume = {},
number = {},
pages = {101203},
doi = {10.1016/j.yfrne.2025.101203},
pmid = {40609837},
issn = {1095-6808},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder affecting 6-13% of reproductive-aged women worldwide. It is primarily characterized by ovarian dysfunction, hyperandrogenism, and metabolic disturbances. However, women with PCOS also face a heightened risk of depression, possibly due to dysregulation in endocrine and immune systems and gut microbiome disturbances. Symptoms of PCOS such as infertility, obesity, and hirsutism can also cause psychological distress and further exacerbate depression symptoms. Despite this comorbidity, mental health aspects of PCOS are often overlooked in the medical field, leading to insufficient support and negative impacts on the quality of life of PCOS patients. This review explores how distinct PCOS phenotypes influence physiological and psychological outcomes and the possible biological mechanisms involved. We also examine the effects of existing treatments on PCOS symptoms and depression. Addressing both physiological and psychological challenges is crucial for developing targeted, personalized interventions that improve outcomes for individuals diagnosed with PCOS.},
}

@article {pmid40609823,
year = {2025},
author = {Spalanzani, RN and Vasconcelos, TM and Bavia, L and Rodrigues, LS and Mesa, D and Fonseca, AS and Cavalli, LR and Dalla-Costa, LM},
title = {Comprehensive overview of the complex gut microbiota-miRNA crosstalk in immunocompromised pediatric patients.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123833},
doi = {10.1016/j.lfs.2025.123833},
pmid = {40609823},
issn = {1879-0631},
abstract = {Immunocompromised pediatric patients, particularly those diagnosed with leukemia, often experience immune suppression due to prolonged use of immunosuppressive medication and chemotherapy. Consequently, these patients are highly vulnerable to infections caused by both pathogenic and non-pathogenic microorganisms. To prevent such infections, antibiotics and antifungals are routinely administered as prophylactic treatments. However, the use of antimicrobials significantly impacts the patient's microbiota, particularly the gut microbiota, which plays a crucial role in immunomodulating the mucosa and maintaining the integrity of the intestinal epithelium. Disruption of these functions may transform the intestinal epithelium into a potential entry point for harmful microorganisms. The regulation of gut homeostasis and the composition of the intestinal microbiota have been linked to different host-derived microRNAs (miRNAs) that regulate gene expression. Intestinal epithelial cells release miRNAs into the lumen, where they modulate the growth of gut microbes and the microbiota's composition. This review summarizes current insights into the relationship between the gut microbiota and intestinal miRNAs, emphasizing their potential as diagnostic and prognostic biomarkers for immunocompromised pediatric patients.},
}

@article {pmid40609813,
year = {2025},
author = {Wang, Y and Wang, X and Xu, X and Liu, M and Wang, J and Ye, H and Zhao, C and Xu, J and Wang, S and Chen, T and Wang, N and Lin, Y and Zheng, W and Bai, Y and Liu, Q},
title = {Sang Zhu Yang Zheng herbal tea: A multi-faceted approach to immunomodulation in the prevention and treatment of respiratory tract infectious diseases.},
journal = {Journal of ethnopharmacology},
volume = {352},
number = {},
pages = {120229},
doi = {10.1016/j.jep.2025.120229},
pmid = {40609813},
issn = {1872-7573},
abstract = {Dysregulation of the upper respiratory tract microbiota, host metabolite profiles, and immune lymphocyte subpopulations is critical in the pathogenesis of respiratory tract infectious diseases (RTIs). Sang Zhu Yang Zheng herbal tea (SZYZ) has emerged as a promising intervention for RTIs, yet its underlying mechanism remains unclear.

AIM OF THE STUDY: This study aims to investigate the immunomodulatory mechanisms of SZYZ underlying its role in the prevention and treatment of RTIs.

MATERIALS AND METHODS: Human studies were conducted to investigate SZYZ's immunomodulatory effects in preventing RTIs in healthy individuals. In healthy human subjects, SZYZ administration was evaluated for its impact on immune cell counts, airway microbiota composition, and metabolic profiles using advanced sequencing and metabonomic techniques. Murine models were utilized to explore SZYZ's preventive and therapeutic effects, as well as its underlying mechanisms against RTIs, with a focus on influenza A virus (IAV) infection. Murine models were employed with H1N1 PR8 virus infection, and study the therapeutic efficacy and mechanisms of SZYZ alone or in combination with oseltamivir.

RESULTS: In healthy humans, SZYZ profoundly increased the total T cells, B cells, CD4[+] T cells, and CD8[+] T cells. 16S rRNA sequencing showed decreased airway microbes' diversity, enrichment of the genera Bacteroides and Bifidobacterium, and lowered phyla Actinobacteria, Synergistetes, and several opportunistic pathogens, including Actinomyces, Fretibacterium, Mobiluncus, and Cloacibacillus, and inhibited microbe functions of human disease and bacterial infectious pathways, after administration. Serum and fecal metabonomic identified changes in 138 and 197 metabolites, respectively. Airway Actinobacteria were negatively corelated to total T cells and CD8[+]T cells count. Serum methyl hexadecanoic acid levels were negatively correlated with T cell counts and positively with Actinobacteria abundance. In IAV-infected mice, SZYZ, administered either as a prophylactic intervention or in combination with oseltamivir, significantly reduced mortality and pathological damage, which were related to immunomodulatory mechanisms of oxidative stress, inflammatory cytokines, and lymphocyte ratio.

CONCLUSION: We comprehensively elucidate the immunomodulatory effects of SZYZ's on microbiota, metabolism, and lymphocyte subpopulations, which provides a new therapeutic approach for the prevention and treatment of RTIs.},
}

@article {pmid40609724,
year = {2025},
author = {Pan, L and Chen, F and Zhao, Q and Yang, J and Qiu, Y and Wu, X and Guan, X},
title = {Soil antimony-microbe interactions in an abandoned antimony mine in southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122268},
doi = {10.1016/j.envres.2025.122268},
pmid = {40609724},
issn = {1096-0953},
abstract = {Soil contamination resulting from antimony (Sb) mining activities poses a substantial environmental risk in karst ecosystems. Understanding microbially mediated Sb transformation mechanisms is critical for advancing eco-friendly remediation technologies. The structural and functional responses of soil microbial communities were systematically investigated across three distinct areas (mining, smelting, and control) in typical Sb mining regions of Southwest China. Integrated geochemical and multi-omics analyses revealed pronounced Sb contamination gradients. Total Sb (Sbtot) concentrations followed the order: smelting area (8,231.97 ± 6,875.22) > mining area (735.03 ± 367.21 mg/kg) > control area (69.11 ± 0.47 mg/kg). Microbial community profiling indicated bacterial dominance (97.6% relative abundance), followed by archaea (2.0%) and fungi (0.4%). Notably, eight bacterial genera (Achromobacter, Sphingomonas, Thermomonas, Janibacter, Stenotrophomonas, Arenimonas, Bifidobacterium, and Halothiobacillus) exhibited significant positive correlations (p < 0.01) with Sbtot concentrations, suggesting their resistance to Sb. Functional annotation revealed critical associations between Sb biotransformation and microbial metabolic pathways, particularly sulfur redox cycling (sulfur oxidation: soxABXYZ; sulfate reduction: dsrAB) and nitrogen metabolism (nitrate reduction: narGHI). Co-occurrence network analysis indicated synergistic relationships between Sb-resistant microbes and elemental-cycling functional genes. Collectively, the results suggest that microbial Sb transformation in karst soils involves sulfur-assisted electron transfer and nitrate-dependent Sb oxidation. This study provides insight into the biogeochemical drivers of Sb fate in contaminated environments and establishes a conceptual framework for the development of microbiome-based remediation strategies suitable for Sb-polluted karst regions.},
}

@article {pmid40609269,
year = {2025},
author = {Wang, X and Zhao, J and Wu, Z and Wang, L and Zhang, W and Zhang, J and Liang, Y},
title = {Bisphenol M exposure promotes adiposity in mice via disrupting hepatic metabolism and gut microbiota homeostasis.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118591},
doi = {10.1016/j.ecoenv.2025.118591},
pmid = {40609269},
issn = {1090-2414},
abstract = {Bisphenol M (BPM), a structural analog of bisphenol A (BPA) commonly used in food packaging and consumer plastics, remains incompletely characterized in terms of its obesogenic potential and underlying molecular mechanisms, posing challenges for evidence-based risk assessment. To address this gap, we investigated the obesogenic effects and metabolic impacts of BPM exposure in male BALB/c mice through integrated liver untargeted metabolomics and gut microbiome analysis. Our results showed that BPM exposure significantly increased body fat percentage, enlarged the epididymal white adipose tissue volume, and induced hepatic steatosis. Untargeted metabolomics revealed that BPM disrupted hepatic metabolic pathways, such as riboflavin metabolism, glycerophospholipid metabolism and fatty acid degradation. Concurrently, BPM altered gut microbiota, increasing the Firmicutes/Bacteroidetes ratio and abundances of Staphylococcus and Jeotgalicoccus. Correlation networks linked these microbial shifts to hepatic lipid metabolites, specifically implicating linoleic acid metabolism as a potential mediator of gut-liver crosstalk in obesity development. These findings indicate that BPM promotes adiposity through liver-gut crosstalk, advancing the understanding of obesogenic risks associated with BPA alternatives.},
}

@article {pmid40609069,
year = {2025},
author = {Jiang, B and Quinn-Bohmann, N and Diener, C and Nathan, VB and Han-Hallett, Y and Reddivari, L and Gibbons, SM and Baloni, P},
title = {Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013253},
doi = {10.1371/journal.pcbi.1013253},
pmid = {40609069},
issn = {1553-7358},
abstract = {The colonic epithelium plays a key role in the host-microbiome interactions, allowing uptake of various nutrients and driving important metabolic processes. To unravel detailed metabolic activities in the human colonic epithelium, our present study focuses on the generation of the first cell-type specific genome-scale metabolic model (GEM) of human colonic epithelial cells, named iColonEpithelium. GEMs are powerful tools for exploring reactions and metabolites at the systems level and predicting the flux distributions at steady state. Our cell-type-specific iColonEpithelium metabolic reconstruction captures genes specifically expressed in the human colonic epithelial cells. iColonEpithelium is also capable of performing metabolic tasks specific to the colonic epithelium. A unique transport reaction compartment has been included to allow for the simulation of metabolic interactions with the gut microbiome. We used iColonEpithelium to identify metabolic signatures associated with inflammatory bowel disease. We used single-cell RNA sequencing data from Crohn's Diseases (CD) and ulcerative colitis (UC) samples to build disease-specific iColonEpithelium metabolic networks in order to predict metabolic signatures of colonocytes in both healthy and disease states. We identified reactions in nucleotide interconversion, fatty acid synthesis and tryptophan metabolism were differentially regulated in CD and UC conditions, relative to healthy control, which were in accordance with experimental results. The iColonEpithelium metabolic network can be used to identify mechanisms at the cellular level, and we show an initial proof-of-concept for how our tool can be leveraged to explore the metabolic interactions between host and gut microbiota.},
}

@article {pmid40608939,
year = {2025},
author = {Argaw-Denboba, A},
title = {The gut microbiome-germline axis: Does a prospective father's gut microbiota matter?.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6755},
pages = {38},
doi = {10.1126/science.adz0492},
pmid = {40608939},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; *Fathers ; *Germ Cells/physiology ; },
abstract = {Does a prospective father's gut microbiota matter?},
}

*Gastrointestinal Microbiome
Humans
Male
*Fathers
*Germ Cells/physiology

@article {pmid40608691,
year = {2025},
author = {Lebeuf-Taylor, E and Cosby, A and Webber, Q and Cottenie, K},
title = {Social structuring of the gut microbiome in communally roosting bats.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0325710},
pmid = {40608691},
issn = {1932-6203},
mesh = {Animals ; *Chiroptera/microbiology/physiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Social Behavior ; },
abstract = {The gut microbiome is the community of microbes that inhabits the gastrointestinal tracts of animals. Laboratory findings have shown that the gut microbiome plays a crucial role in host metabolism, physiology, and immunity. This has led to speculation that selection acts on both host and microbiome-although identifying functionally essential coevolving microbes in wild animals remains challenging. A recent surge of studies in wild populations has identified phylogenetic, spatiotemporal, dietary, and social patterns in host-associated microbiomes. Here, we describe and assess the gut microbiomes of two sympatric bat species: big brown bats (Eptesicus fuscus) and little brown bats (Myotis lucifugus). Although these species share similar diets and environments throughout much of their North American ranges, we found they have distinct gut microbiomes. We find no evidence of a functional core microbiome among big brown bats and identify roost identity as a driver of microbiome composition, likely arising from social transmission among hosts through physical proximity. We conclude that both environmental and social factors drive microbiome composition in big brown bats and that repeated, extensive sampling is required to bring ecological reality to host-associated microbiome studies in wild populations.},
}

Animals
*Chiroptera/microbiology/physiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Phylogeny
*Social Behavior

@article {pmid40608175,
year = {2025},
author = {Ye, Z and Yu, Y and Cao, Z and Ye, Z and Gu, X and Shen, X and Cai, B and Lin, B and Ji, C and Qiao, N and Wu, Z and Chen, Z and Ma, Z and Chen, L and Liang, B and Liao, Y and He, W and Shen, Q and Han, J and Cao, X and Zhou, X and Shou, X and Shen, M and Wang, Y and Zhang, Z and Ye, H and Zhang, Q and Gao, R and Zhang, Y},
title = {Microbiome and metabolic disorder in prolactinoma: intrinsic gender differences and extrinsic therapy effects.},
journal = {Pituitary},
volume = {28},
number = {4},
pages = {83},
pmid = {40608175},
issn = {1573-7403},
support = {24ZR1408900//Natural Science Foundation of Shanghai Municipality/ ; 320.6750.2023-13-11//Wu Jieping Medical Foundation/ ; 2023ZD0506800//National Major Science and Technology Projects of China/ ; 82202906//National Natural Science Foundation of China/ ; },
}

@article {pmid40608163,
year = {2025},
author = {Li, MX and Lian, WH and Lian, ZH and Luo, XQ and Yue, LX and Han, JR and Hu, CJ and Li, S and Li, WJ and Dong, L},
title = {Rare and abundant taxa in Artemisia desertorum rhizosphere soils demonstrate disparate responses to drought stress.},
journal = {Advanced biotechnology},
volume = {3},
number = {3},
pages = {21},
pmid = {40608163},
issn = {2948-2801},
support = {32270076//National Natural Science Foundation of China/ ; 2022xjkk1200//The Third Xinjiang Scientific Expedition Program/ ; 2022B0202110001//Guangdong S&T Program/ ; },
abstract = {The growth and adaptability of desert plants depend on their rhizosphere microbes, which consist of a few abundant taxa and numerically dominant rare taxa. However, the differences in diversity, community structure, and functions of abundant and rare taxa in the rhizosphere microbiome of the same plant in different environments remain unclear. This study focuses on the rhizosphere microbial communities of Artemisia desertorum, a quintessential desert sand-stabilizing plant, investigating the diversity patterns and assembly processes of rare and abundant taxa across four Chinese deserts: Mu Us, Kubuqi, Tengger, and Ulan Buh. The results show that climatic factors, especially aridity and mean annual precipitation (MAP), significantly influence bacterial community composition and microbial network complexity. The interactions between rare and non-rare taxa are non-random, forming a modular network in which rare taxa serve as central nodes, and their loss could destabilize the network. Rare taxa are primarily shaped by heterogeneous selection, whereas abundant taxa are mainly influenced by dispersal limitation. Functionally, abundant taxa exhibit higher metabolic potential, whereas rare taxa are more involved in processes such as cell motility, indicating distinct ecological roles. These results provide new insights into the ecological functions of rare and abundant taxa in desert rhizosphere communities and highlight the importance of microbial management for desert plant health.},
}

@article {pmid40607846,
year = {2025},
author = {Carvalho, T and Medina, D and James, TY},
title = {Successful Transmission and Isolation of a Fungal Pathogen From Wild Frogs to a Captive Amphibian Model Species: Fine Scale Pathogen Genetic Diversity and Infection-Induced Changes in Skin Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70136},
pmid = {40607846},
issn = {1462-2920},
support = {9337//Gordon and Betty Moore Foundation/ ; //Canadian Institute for Advanced Research/ ; },
mesh = {Animals ; *Batrachochytrium/genetics/isolation & purification ; *Skin/microbiology ; *Genetic Variation ; *Anura/microbiology ; *Mycoses/microbiology/veterinary/transmission ; *Bacteria/isolation & purification/classification/genetics ; *Chytridiomycota/genetics/isolation & purification ; Genotype ; Animals, Wild/microbiology ; },
abstract = {Amphibian populations worldwide are severely threatened, in part, by the pathogenic fungus Batrachochytrium dendrobatidis (Bd). While Bd has driven many amphibian declines and extinctions, its impact varies, with some populations exhibiting resistance or tolerance. Understanding the mechanisms behind this variation, together with Bd genetic diversity, is crucial for conservation. We used the model organism Hymenochirus boettgeri in a lab-based transmission experiment designed to isolate Bd derived from wild amphibian hosts with low pathogen loads. Through successful transmission and subsequent isolation and genotyping, we identified multiple Bd genotypes from a single population, including a potential sexual recombinant, all belonging to the Global Panzootic Lineage (Bd-GPL). This finding contributes to evidence of ongoing genetic mixing of Bd in natural environments. Additionally, we leveraged this experiment to assess Bd-induced changes in amphibian skin bacteria. Our results showed significant changes in the skin bacterial communities of H. boettgeri after acquiring Bd infection, including reductions in bacterial diversity, and shifts in community composition, as observed in others susceptible species. These findings highlight the value of transmission experiments in isolating Bd from wild hosts and underscore the potential of H. boettgeri as a model to investigate Bd genetic diversity and host-associated microbiome responses to infection.},
}

Animals
*Batrachochytrium/genetics/isolation & purification
*Skin/microbiology
*Genetic Variation
*Anura/microbiology
*Mycoses/microbiology/veterinary/transmission
*Bacteria/isolation & purification/classification/genetics
*Chytridiomycota/genetics/isolation & purification
Genotype
Animals, Wild/microbiology

@article {pmid40607829,
year = {2025},
author = {Williams, A and Ravel, J and Armstrong, E and Huibner, S and Rutt, L and Kaul, R and Holm, JB},
title = {Temporal dynamics of the vaginal microbiome and host immune markers before, during, and after metronidazole treatment for bacterial vaginosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0038025},
doi = {10.1128/msystems.00380-25},
pmid = {40607829},
issn = {2379-5077},
abstract = {This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV-associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify the optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.IMPORTANCEBacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections, among others, is characterized by a dysbiotic vaginal microbiome associated with the predominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at the initiation of treatment, as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during, and after metronidazole treatment.},
}

@article {pmid40607612,
year = {2025},
author = {Angot, V and Thiour-Mauprivez, C and Schellenberger, R and Lamboeuf, M and Crépin, O and Garmyn, D and Blouin, M and Jacquiod, S},
title = {Alleviation of water-deficit inhibition of plant growth by rhizosphere microbiota conditioning.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70362},
pmid = {40607612},
issn = {1469-8137},
support = {//University of Bourgogne Franche-Comté via an ISITE-BFC International Junior Fellowship Award/ ; ANR-11-INBS-0012//Agence Nationale de la Recherche, Programme Investissements d'avenir/ ; },
abstract = {Rhizosphere microbiota conditioning is a promising strategy to enhance plant growth. We conditioned the rhizosphere microbiota of Brassica juncea to water deficit to assess its impact on plant growth. In a glasshouse, plants were first grown under well-watered conditions, then exposed to moderate (MD, pF = 2.3) or extreme (ED, pF = 3.5) water deficits. We extracted and inoculated the rhizosphere microbiota to new plants and repeated this process 10 times. Control plants were kept well-watered. We monitored changes in plant phenotypes and in rhizosphere microbial communities (bacteria and eukaryotes). The initial water-deficit growth inhibition of plants was successfully alleviated by 19.3% in MD and 29.4% in ED after conditioning (MD: from -35.6% to -16.3%; ED: from -56.8% to -27.4%). This beneficial effect on plants was not observed during the well-watered phases, suggesting an active role of the microbiota when water became scarce. The increase in plant growth correlated with aggregated rhizosphere soil and significantly matched changes in the bacterial community, featuring reduced diversity and increased biofilm production capacity along the conditioning process. We showed that microbiota conditioning was a fast and efficient way to achieve better plant growth under adverse conditions, likely via the adaptation capabilities of the rhizosphere bacterial community.},
}

@article {pmid40607437,
year = {2025},
author = {Qi, P and Li, L and Zhang, J and Ren, L and Xie, X},
title = {The dual regulatory effects of intestinal microorganisms and their metabolites in gouty arthritis pathogenesis: a balance between promotion and inhibition.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1591369},
pmid = {40607437},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Arthritis, Gouty/microbiology/metabolism/immunology/etiology ; Animals ; Uric Acid/metabolism ; *Bacteria/metabolism ; },
abstract = {Gout is an arthritis characterized by the deposition of urate crystals, often accompanied by robust inflammatory responses. The gut microbiome profoundly influences gout pathogenesis, progression, and management by affecting uric acid metabolism, immune responses, and intestinal barrier function. Studies reveal that gut microorganisms exert a dual role in gout development. Gout patients typically exhibit increased harmful bacterial abundance and reduced beneficial species. Harmful bacteria and associated metabolites can influence systemic uric acid levels by regulating excretion and synthesis, thereby promoting gout manifestations. Conversely, beneficial bacteria interact with the host immune system to inhibit inflammation and modulate the inflammatory state of joints. Furthermore, the gut microbiome can significantly impact gout treatment efficacy through its influence on drug metabolism and absorption. Research highlighting the gut-joint-inflammation axis offers novel therapeutic strategies for gout, suggesting that future approaches may involve microbiome modulation to enhance clinical outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Arthritis, Gouty/microbiology/metabolism/immunology/etiology
Animals
Uric Acid/metabolism
*Bacteria/metabolism

@article {pmid40607421,
year = {2025},
author = {Fraser, DR and Stadnyk, AW},
title = {The emerging relationship between mucosal-associated invariant T cell populations and the onset and progression of type 1 diabetes.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1602934},
pmid = {40607421},
issn = {1664-3224},
mesh = {*Diabetes Mellitus, Type 1/immunology/pathology/metabolism/etiology ; Humans ; *Mucosal-Associated Invariant T Cells/immunology/metabolism ; Animals ; Disease Progression ; Gastrointestinal Microbiome/immunology ; Mice ; },
abstract = {Type 1 diabetes (T1D) is a chronic autoimmune disorder characterized by autoreactive CD8[+] T cells that destroy insulin-producing pancreatic β-cells. CD8[+] T cells are unlikely to be the only cells involved in diabetes. Relatively recently described and still enigmatic, Mucosal-associated invariant T (MAIT) cells, innate-like T cells that recognize microbial-derived peptides, exist in the blood and tissues and are implicated in early immune responses. Immunological differences, some of which implicate MAIT cells, exist between individuals at different stages of T1D progression. This review explores the emerging relationship between gastrointestinal and pancreatic MAIT cell populations and the onset and progression of T1D. Early microbial colonization is critical for immune maturation, homeostasis, and MAIT cell development, and disruptions such as Caesarean delivery or antibiotic-induced dysbiosis correlate with increased T1D incidence. Diabetes progression in the diabetes-prone NOD mice is associated with reduced gut mucosal integrity, impairing the protective IL-17 and IL-22 responses of gut-resident MAIT cells and exacerbating systemic inflammation. MAIT cells recruited to the inflamed pancreas during T1D onset likely contribute to β-cell destruction through IFN-γ and granzyme B production. This hypothesis is supported by altered MAIT cell frequencies and phenotypes in individuals with T1D; MAIT cells are reduced in the blood of children recently diagnosed with T1D, potentially corresponding to pancreatic migration, while adults with long-term T1D have persistent, circulating MAIT cells with exhaustion markers. MAIT cells appear to have dual protective and pathogenic roles impacted by microbiome interactions. Understanding these relationships may inform non-invasive biomarkers for the disease.},
}

*Diabetes Mellitus, Type 1/immunology/pathology/metabolism/etiology
Humans
*Mucosal-Associated Invariant T Cells/immunology/metabolism
Animals
Disease Progression
Gastrointestinal Microbiome/immunology
Mice

@article {pmid40607345,
year = {2025},
author = {Huang, HW and Kuo, TC and Lee, YJ and Chen, MJ},
title = {Multi-omics analysis reveals the efficacy of two probiotic strains in managing feline chronic kidney disease through gut microbiome and host metabolome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1590388},
pmid = {40607345},
issn = {2297-1769},
abstract = {Gut dysbiosis has been implicated in the progression of chronic kidney disease (CKD), yet the functional alterations of the microbiome and their links to host metabolism in feline CKD pathophysiology remain unclear. Our previous findings suggested that Lactobacillus mix (Lm) may mitigate CKD progression by modulating gut microbiota composition and restoring microbial balance. In this pilot study, we aimed to evaluate the potential effects of an 8-week Lm intervention in cats with stage 2-3 CKD and to investigate the underlying host-microbiota interactions through integrated multi-omics analysis. We performed full-length 16S rRNA amplicon sequencing and untargeted metabolomics to characterize the intricate interactions between the gut microbiome and host metabolome, and further investigate the modulation of microbial function and its related gut-derived metabolites before and after the intervention. During this period, creatinine and blood urea nitrogen levels were stabilized or reduced in most cats, and gut-derived uremic toxins (GDUTs) showed modest numerical reductions without statistically significant changes. Lm intervention was also associated with increased gut microbial diversity, alterations in specific bacterial taxa, and upregulation of microbial functions involved in GDUTs and short-chain fatty acid (SCFAs) biosynthesis pathways. To further explore individual variations in response, we conducted a post hoc exploratory subgroup analysis based on changes in microbial-derived metabolites. Cats classified as high responders, defined as those with reductions in three GDUTs and increases in SCFAs, exhibited distinct microbiome compositions, microbial functional profiles, and metabolite shifts compared to moderate responders. Among high responders, modulation of microbial pathways involved in GDUTs (tyrosine, tryptophan, and phenylalanine metabolism) and SCFAs (pyruvate, propanoate, and butanoate metabolism) biosynthesis was particularly evident. Notably, the relative abundance of Lm strains was higher in high responders, suggesting a potential association between colonization efficiency and microbial metabolic outcomes. This study demonstrates an Lm-mediated interconnection between the modulation of microbial composition, metabolic functions, and systemic metabolite profiles. Overall, our findings suggest that Lm intervention may influence the gut-kidney axis in cats with CKD. These preliminary, hypothesis-generating results highlight the value of multi-omics approaches for understanding host-microbe interactions and support further investigation into personalized probiotic strategies as potential adjuvant therapies in feline CKD.},
}

@article {pmid40607343,
year = {2025},
author = {Xu, H and Zhang, F and Che, Y and Cui, Y and Yao, Q and Guan, Y and Chen, H and Huang, Y},
title = {Integrative multi-omics and bioinformatics analysis of the effects of BaiRui YuPingFeng Powder on intestinal health in broilers.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1606531},
pmid = {40607343},
issn = {2297-1769},
abstract = {INTRODUCTION: In recent years, global poultry consumption has increased rapidly, making chicken the most widely consumed meat worldwide by 2019. To increase livestock development, antibiotics are often added to animal feed as growth promoters. But overuse of antibiotics may alter the gut microbiota, make people more resistant to them, and raise the possibility that they will spread antibiotic resistance genes to the human microbiome. Therefore, identifying safe and effective alternatives to antibiotics in livestock production is crucial for maintaining and improving gut microbial balance, ultimately promoting poultry health. The aim of this study was to investigate the mechanisms behind the impacts of BaiRui YuPingFeng Powder (TCYP) on intestinal health in broilers using combined metabolomics, bioinformatics analysis, and 16S rRNA sequencing.

METHODS: In a 42-day feeding trial, 300 one-day-old broilers were randomly divided into five groups (six replicates per group; 10 broilers per replicate) fed a basal diet with or without supplements: control (CON), antibiotic (ATB), and TCYP at 500, 1000, and 1500 mg/kg. Growth performance, serum biochemical parameters, intestinal morphology, cecal microbiota composition, and metabolomic profiles were analyzed. Bioinformatics analysis was used to identify potential targets and pathways, followed by qPCR validation of key genes.

RESULTS: Compared with the CON group, TCYP administration dose-dependently reduced the feed-to-gain ratio (F/G) and average daily feed intake (ADFI) while increasing average daily gain (ADG), with the high-dose TCYP showing more pronounced effects (p < 0.05). Serum biochemical analysis revealed that TCYP treatment significantly decreased serum levels of total cholesterol (T-CHO), triglycerides (TG), lactate dehydrogenase (LDH), and alanine aminotransferase (ALT) in a dose-dependent manner, while elevating albumin (ALB) content. These beneficial effects were particularly marked in the high-dose TCYP group (p < 0.05). Histopathological examination indicated that high-dose TCYP significantly enhanced villus height and the villus-to-crypt ratio (V/C) in the duodenum, jejunum, and ileum compared to the CON group (p < 0.05). 16S rRNA sequencing analysis revealed that TCYP treatment significantly modified the β-diversity of cecal microbiota (p < 0.01). Compared to the CON group, ATB treatment increased the abundance of Faecalibacterium and Lachnospiraceae_unclassified but reduced Ruminococcaceae_unclassified and Firmicutes_unclassified. Notably, dietary TCYP supplementation maintained gut microbiota profiles similar to the CON group, demonstrating its stabilizing effect on microbial community structure in broilers. Metabolomic analysis identified differential metabolites primarily involved in lipid and lipid-like molecules, organic heterocyclic compounds, and organic acids and derivatives. Spearman correlation analysis revealed significant associations between Lachnospiraceae_unclassified and metabolites such as Gly-Leu, fumarate, and phenylpyruvic acid (|r| > 0.5, p < 0.05). Bioinformatics analysis suggested that TCYP may improve intestinal health by regulating key targets, including MMP9, TGFB1, and PPARG, as well as the peroxisome proliferator-activated receptor (PPAR) signaling pathway. Quantitative PCR (qPCR) results showed that, compared to the CON group, TCYP dose-dependently significantly upregulated the mRNA expression of PPARG, PDPK1, and Bcl2 in jejunal tissues (p < 0.05), while significantly downregulating the expression of MMP1 and Bax (p < 0.05).

CONCLUSION: TCYP enhances growth performance and intestinal health in broilers through multiple mechanisms, including maintaining cecal microbial homeostasis, modulating lipid and amino acid metabolism, with potential involvement of the PPAR signaling pathway based on bioinformatics and gene expression analysis.},
}

@article {pmid40607325,
year = {2025},
author = {Sekar, R and Bottu, K and Gb, P and Ramasamy, J and Venkatesalu, B},
title = {Comparative analysis of candidal carriage rates in long-term and short-term COVID-19 patients: An RT-PCR study.},
journal = {Journal of oral biology and craniofacial research},
volume = {15},
number = {4},
pages = {899-904},
pmid = {40607325},
issn = {2212-4268},
abstract = {BACKGROUND: Most individuals who had COVID-19 infection recover completely. However, current research shows that 10-20 % of the population, especially immunocompromised and elderly people, endure numerous adverse effects and multiple complications associated with different organs and systems during its pathogenic cycle. Also, many fungal coinfections are seen as post-COVID dysbiosis, the most common fungal organism being Candida. This study aims to compare the candidal carriage rate of short-term and long-term affected SARS-COV-2 patients in saliva using PCR and compare it with healthy individuals.

RESULTS: The study included both male (15) and female (23) long-term and short-term post-COVID patients and healthy individuals [Male (5) and Female (15)]. The candidal carriage rate was increased in long-term COVID patients than in short-term COVID patients and healthy individuals (p < 0.001∗). Among long-term COVID patients, those who had oxygen assistance (p=0.04) and were admitted to the ICU (p=0.01) had relatively higher candidal carriage rates than those who didn't receive any intensive care procedures.

CONCLUSION: COVID-19 significantly affects the oral microbiome, leading to dysbiosis and increased candidal carriage. The manifestation of fungal coinfections in post-COVID patients appears to be influenced by various factors, including oxygen support, catheterization, and immunosuppressive treatments. Thereby, early diagnosis and early intervention, along with health care providers acquainted with potential risks and the likelihood of secondary infections, are the only ways to reduce the consequences of this devastating disease.},
}

@article {pmid40607028,
year = {2025},
author = {Yin, X and Tian, L and Liu, Q and Zhao, H},
title = {Association between pro-inflammatory diet and ulcerative colitis: a systematic review and meta-analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1586691},
pmid = {40607028},
issn = {2296-861X},
abstract = {BACKGROUND: Emerging evidence suggests that dietary patterns can mediate intestinal inflammatory responses through immune-microbiome interactions. Diet and inflammation are important pathogenic factors for ulcerative colitis (UC). However, the existing evidence regarding the association between a pro-inflammatory diet and the risk of UC is controversial, and further clarification of this association is needed.

OBJECTIVE: This study aimed to explore the association between pro-inflammatory diet and UC risk.

METHODS: We systematically searched PubMed, Web of Science, Scopus, EMBASE, and Cochrane Library databases from their inception to January 15th, 2025. Two researchers independently used the Newcastle - Ottawa Scale to assess the quality of the included studies. Data analysis was performed using STATA 17 software.

RESULTS: This systematic review and meta-analysis included eight studies involving approximately 758,068 participants. The meta-analysis indicated that an inflammatory or pro-inflammatory diet did not increase the risk of UC (OR = 0.97, 95% CI = 0.84-1.12). However, subgroup analyses revealed differing results: within the case-control study subgroup, a pro-inflammatory diet was associated with an increased risk of UC (OR = 2.09, 95% CI: 1.23-3.56), whereas in the cohort study subgroup, no significant association was found between a pro-inflammatory diet and UC (OR = 0.91, 95% CI: 0.78-1.06). Sensitivity analysis indicated that the study results were robust. Additionally, Begg's test (p = 0.174) and Egger's test (p = 0.085) showed no significant publication bias in this study.

CONCLUSION: The results of this study do not support a significant association between pro-inflammatory diets and UC risk. However, due to the limited level of evidence from observational studies and their heterogeneity, the association between pro-inflammatory diets and UC may be underestimated or overestimated. Therefore, larger multi-centre studies are needed to standardize the assessment of diets and adjust for microbial-related confounding factors in order to elucidate the association and mechanisms between pro-inflammatory diets and UC.},
}

@article {pmid40607026,
year = {2025},
author = {Yang, X and Li, H and Qumu, D and Han, B and Amatjan, M and Wu, Q and Wei, L and Li, B and Ma, M and He, J and Wang, S and Yu, Y and Shao, X},
title = {Taurine alleviates hyperuricemia-induced nephropathy in rats: insights from microbiome and metabolomics.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1587198},
pmid = {40607026},
issn = {2296-861X},
abstract = {BACKGROUND: Gut microbiota play a critical role in developing hyperuricemic nephropathy (HN). We previously found that sulfur-containing amino acid taurine (T) has nephroprotective effects in hyperuricemia (HUA) rats. However, the mechanism is still unclear. To investigate the underlying mechanism of T, rats were fed adenine and ethambutol hydrochloride for the introduction of HN.

METHODS: Pathological changes in the kidney were assessed using hematoxylin and eosin staining. 16S rRNA sequencing and metabolomics analyzed changes in the gut microbiota and fecal metabolism, and in vitro experiments were conducted to investigate the potential action and mechanism of T against HN.

RESULTS: In vitro results demonstrated that T could inhibit NF-κB, IL-1β, IL-6, TNF-α, and ROS in UA-induced HK-2 cells. It also improved renal function, ameliorated renal fibrosis, and reversed enteric dysbacteriosis in HN rats. These results showed that T protects against HN through the modulation of metabolites mediated by the gut microbiota. Meanwhile, gut microbiota included Lactobacillus and Lachnospiraceae NK4A136 group showed correlations with nephroprotective profiles of T. The combined analysis of 16S rRNA gene sequencing and untargeted metabolomics indicated that the anti-HN effects of T could be achieved through phenylalanine metabolism, caffeine metabolism, nicotinate and nicotinamide metabolism, retinol metabolism, and tryptophan metabolism.

CONCLUSION: These findings suggest that the potential protective mechanism of T for HN is not only related to altered metabolic pathways and downregulation of inflammatory cytokines but also to the reciprocal regulation of microbiota structure and metabolism.},
}

@article {pmid40606980,
year = {2025},
author = {Kim, Y and Kim, MK and Lee, S},
title = {Comparative microbiome analysis of paired mucosal and fecal samples in Korean colorectal cancer patients.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1578861},
pmid = {40606980},
issn = {2234-943X},
abstract = {BACKGROUND: Colorectal cancer (CRC) is increasingly linked to gut microbiome dysbiosis. However, few studies have examined tumor-associated microbial dynamics in Korean CRC patients using both mucosal and fecal samples.

METHODS: We analyzed paired fecal and mucosal samples from 30 Korean CRC patients aged 60-80 years before and after surgery. Microbial DNA was sequenced using 16S rRNA gene analysis. Diversity metrics, differential abundance testing (LEfSe), and pathway prediction (PICRUSt2) were performed. Diagnostic performance was evaluated with ROC curves, and associations with clinical parameters were assessed via regression models.

RESULTS: Beta diversity revealed significant compositional differences between fecal and mucosal samples (p = 0.001), with mucosal samples showing higher enrichment of CRC-associated taxa. Fusobacterium, Prevotella 9, Parvimonas, and Holdemanella were significantly enriched in pre-surgical samples and declined after surgery (p < 0.01). Combined microbial markers yielded an AUC of 0.841 for distinguishing pre- from post-surgical status. Functional predictions indicated upregulation of amino acid metabolism and lipopolysaccharide (LPS) biosynthesis pathways in pre-surgical samples. Notably, Fusobacterium abundance correlated with TNM stage (p = 0.028), and Prevotella 9 abundance decreased with age (p = 0.006).

CONCLUSION: This study highlights distinct microbial and functional signatures in CRC, particularly from mucosal samples, which offer deeper insights into tumor-microbiota interactions. The identified microbial markers and enriched pathways may contribute to immune modulation and tumor progression. These findings support the potential for microbiome-based diagnostic and therapeutic strategies tailored to Korean CRC patients and underscore the importance of dual-sample analysis in microbiome research.},
}

@article {pmid40606926,
year = {2025},
author = {Pandey, H and Goel, P and Srinivasan, VM and Tang, DWT and Wong, SH and Lal, D},
title = {Gut microbiota in non-alcoholic fatty liver disease: Pathophysiology, diagnosis, and therapeutics.},
journal = {World journal of hepatology},
volume = {17},
number = {6},
pages = {106849},
pmid = {40606926},
issn = {1948-5182},
abstract = {Non-alcoholic fatty liver disease (NAFLD), also referred to as metabolic-associated fatty liver disease, is among the most prevalent chronic liver conditions. In some cases, NAFLD may lead to liver inflammation and non-alcoholic steatohepatitis, which can eventually progress to liver cirrhosis and hepatocellular carcinoma. The pathophysiology of NAFLD is complex, involving both genetic and environmental factors. NAFLD is a multisystem disease linked to a higher likelihood of developing metabolic disorders such as type 2 diabetes, obesity, and cardiovascular and chronic kidney diseases. The gut-liver axis represents a key connection between the gut microbiota and the liver, and its disruption has been linked to NAFLD. Growing evidence underscores the significant role of gut microbiota in the onset and progression of NAFLD, with alterations in the gut microbiome and impaired gut barrier function. Studies have identified key microbiota signatures and metabolites linked to NAFLD, implicating oxidative stress, endotoxemia, and inflammatory pathways that further strengthen the connection between gut microbiota and NAFLD. Modulation of gut microbiota through diet and microbiota-centered therapies, such as next-generation probiotics and fecal microbiota transplantation, holds promise for treating NAFLD. In this review, we explore the key link between gut microbiota and the development and progression of NAFLD, as well as its potential applications in the diagnosis and treatment of the disease.},
}

@article {pmid40606636,
year = {2025},
author = {Lin, SH and Lin, RJ and Chan, KY and Chu, CL and Chen, YL and Fu, SC},
title = {Anxiety-related gut microbiota alterations in Parkinson's disease: distinct associations compared to healthy individuals.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594152},
pmid = {40606636},
issn = {2235-2988},
mesh = {Humans ; *Parkinson Disease/microbiology/complications/psychology ; *Gastrointestinal Microbiome ; *Anxiety/microbiology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Aged ; Middle Aged ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis ; },
abstract = {BACKGROUND AND OBJECTIVES: Anxiety affects 25-49% of Parkinson's disease (PD) patients, exacerbating non-motor symptoms and significantly reducing quality of life. Growing evidence suggests that gut microbiota plays a role in anxiety, but whether its impact differs between PD and non-PD populations remains unclear. This study explores the heterogeneity of gut microbiota-associated anxiety in PD and non-PD individuals.

METHODS: Participants from the NeuroGenetics Research Consortium provided clinical data, including PD status, anxiety status, and stool samples analyzed via 16S rRNA sequencing. After excluding nine participants with missing anxiety data, 322 individuals were included (193 PD, 129 non-PD). We assessed α-diversity, β-diversity, taxonomic composition, and functional pathways to compare microbial differences between anxious and non-anxious individuals within and across PD and non-PD groups.

RESULTS: Beta diversity analysis revealed significant microbial differences between anxious and non-anxious PD patients (p = 0.043 in Bray-Curtis index) but not in the non-PD group. Escherichia-Shigella was significantly enriched in non-anxious PD patients (p = 0.011). Functional pathway analysis identified distinct metabolic alterations associated with anxiety in PD and non-PD individuals. In non-PD participants, anxiety was linked to increased activity in glycosphingolipid biosynthesis, sphingolipid metabolism, other glycan degradation, glycosphingolipid biosynthesis, and glycosaminoglycan degradation. In contrast, PD patients with anxiety exhibited enrichment in indole alkaloid biosynthesis, linoleic acid metabolism, and polyketide sugar unit biosynthesis.

CONCLUSION: Gut microbiota-associated anxiety differs between PD and non-PD populations, suggesting distinct pathophysiological mechanisms. These findings underscore the potential of microbiome-targeted interventions as novel therapeutic strategies for anxiety in PD patients.},
}

Humans
*Parkinson Disease/microbiology/complications/psychology
*Gastrointestinal Microbiome
*Anxiety/microbiology
Male
Female
RNA, Ribosomal, 16S/genetics
Aged
Middle Aged
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Dysbiosis