@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

@article {pmid40606566,
year = {2025},
author = {Wang, L and Wang, L and Chen, L},
title = {NetNiche: Microbe-Metabolite Network Reconstruction and Microbial Niche Analysis.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {2},
pages = {208-211},
pmid = {40606566},
issn = {2730-5848},
abstract = {UNLABELLED: Metagenomics and metabolomics technologies have been widely used to investigate the microbe-metabolite interactions in vivo. However, the computational methods that accurately infer the microbe-metabolite interactions are lacking. We present a context-aware framework for graph representation learning, NetNiche, which predicts microbe-metabolite and microbe-microbe interactions in an accurate manner, by integrating their abundance data with prior knowledge. We applied NetNiche to datasets on gut and soil microbiome, and demonstrated that NetNiche can outperform the state-of-the-art methods, such as SParse InversE Covariance Estimation for Ecological Association Inference (SPIEC-EASI), Sparse Correlations for Compositional data (SparCC) and microbe-metabolite vectors (mmvec). NetNiche is an effective tool with wide applicability for the multi-omics study of human microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00168-8.},
}

@article {pmid40606527,
year = {2025},
author = {Paaske, SE and Baunwall, SMD and Rubak, T and Rågård, N and Kelsen, J and Hansen, MM and Lødrup, AB and Erikstrup, LT and Mikkelsen, S and Erikstrup, C and Dahlerup, JF and Hvas, CL},
title = {Clinical management of Clostridioides difficile infection with faecal microbiota transplantation: a real-world cohort study.},
journal = {EClinicalMedicine},
volume = {85},
number = {},
pages = {103302},
pmid = {40606527},
issn = {2589-5370},
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) causes high morbidity and mortality. Faecal microbiota transplantation (FMT) is well-established for CDI, but therapeutic strategies may be optimised. We aimed to evaluate clinical outcomes by analysing therapeutic strategies in a real-life cohort of patients with CDI treated with FMT.

METHODS: We conducted a multi-site cohort study, including 1170 patients with CDI, treated with FMT through capsules, colonoscopy, or nasojejunal tube between May 2016 and December 2023. The primary outcome was cure of C. difficile-associated diarrhea (CDAD) eight weeks after treatment. We investigated antibiotic pretreatment type and length, FMT dosing and administration, and post-FMT prophylactic vancomycin during non-CDI antibiotic use, applying multivariable mixed-effect regression analysis including the patient as a random effect. The study was preregistered at ClinicalTrials.gov, NCT03712722.

FINDINGS: The 1170 patients received 1643 FMT treatments. Patients' median age was 71 years (interquartile range 56-80 years). Following their first FMT treatment, 699 patients (60% (95% confidence interval: 57-63%)) were cured of CDAD. After repeated FMT treatments, 944 patients (81% (78-83%)) were cured. Prolonged antibiotic pretreatment was associated with higher cure rates (65% (59-70%), odds ratio (OR): 1.22 (1.10-1.36), p < 0.001). FMT administration through oral, multi-dose capsules (69% (63-74%), OR: 1.19 (1.11-1.27), p < 0.001) or colonoscopy (69% (61-76%), OR: 1.14 (1.04-1.24), p = 0.01) resulted in the highest cure rates. Neither antibiotic pretreatment type nor prophylactic vancomycin during non-CDI antibiotics affected cure rates. In patients for whom FMT was initially unsuccessful, repeated FMT was more effective than antibiotic treatment alone.

INTERPRETATION: CDI outcomes could be improved by optimising antibiotic pretreatment duration, selecting appropriate FMT delivery methods, and repeating FMT.

FUNDING: Innovation Fund Denmark (j.no. 8056-00006B).},
}

@article {pmid40606170,
year = {2025},
author = {Slater, FC and Fish, KE and Boxall, JB},
title = {Similarity of drinking water biofilm microbiome despite diverse planktonic water community and quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1567992},
pmid = {40606170},
issn = {1664-302X},
abstract = {The impact of drinking water quality, in particular the planktonic microbiome, on the bacterial and fungal community composition of biofilms in drinking water infrastructure is explored. Understanding drinking water biofilms is critical as biofilms can degrade water quality and potentially present a public health risk if pathogens are released. Biofilms were developed for 12 months in three state-of-the-art pipe loop facilities installed at water treatment works and hence supplied by distinct treated drinking water and unique planktonic bacterial and fungal microbiomes. Each pipe loop had identical physical conditions, including pipe diameter, material and hydraulic regime (shear stress and turbulence). Despite the different bulk-waters, the bacterial and fungal community composition of the biofilm within each loop were remarkably similar, although in different quantities. The similarity between the biofilms from unique systems, with significantly different planktonic microbiomes, suggests shared selective pressures across the different sites which are independent of the varying water qualities, including planktonic community. This suggests that taking a global view of biofilm microbiome management is potentially feasible and that approaches controlling material or hydraulics may be best way to do this.},
}

@article {pmid40606169,
year = {2025},
author = {Mallick, S and Pavloudi, C and Saw, J and Eleftherianos, I},
title = {Heterorhabditis bacteriophora symbiotic and axenic nematodes modify the Drosophila melanogaster larval microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1598221},
pmid = {40606169},
issn = {1664-302X},
abstract = {The Drosophila melanogaster microbiome is crucial for regulating physiological processes, including immune system development and function. D. melanogaster offers distinct advantages over vertebrate models, allowing a detailed investigation of host-microbiota interactions and their effects on modulating host defense systems. It is an outstanding model for studying innate immune responses against parasites. Entomopathogenic nematodes (EPNs) activate immune signaling in the fly, leading to immune responses to combat infection. However, the impact of EPN infection on the host larval microbiome remains poorly understood. Therefore, we investigated whether EPN infection affects the D. melanogaster larval microbiome. We infected third-instar D. melanogaster larvae with Heterorhabditis bacteriophora symbiotic nematodes (containing Photorhabdus luminescens bacteria) and axenic nematodes (devoid of symbiotic bacteria). Drosophila melanogaster microbiome analysis revealed statistically significant differences in microbiome composition between uninfected and EPN-infected larvae. Notably, infection with axenic nematodes resulted in 68 unique species, causing a significant shift in the D. melanogaster larval microbiome and an increase in bacterial diversity compared to larvae infected with symbiotic nematodes. This suggests that the absence of the endosymbiont creates ecological niches for unique species and a more diverse microbiome in larvae infected with the axenic nematodes. This research will enhance our understanding of microbial species within the D. melanogaster microbiome that regulate homeostasis during nematode infection. These insights could be beneficial in developing innovative strategies for managing agricultural pests and disease vectors.},
}

@article {pmid40606166,
year = {2025},
author = {Hong, S and Xing, Y and Yang, J and Zhao, Q and Su, F and Zhuang, H and Wang, H and Wu, Z and Chen, Y},
title = {Pandan-vanilla rotation mitigates Fusarium wilt disease in vanilla: insights from rhizosphere microbial community shifts.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496701},
pmid = {40606166},
issn = {1664-302X},
abstract = {INTRODUCTION: Vanilla monoculture often leads to Fusarium wilt disease, affecting the industry globally.

METHODS: Here, we evaluated the effects of vanilla-black pepper, -pandan, and -sweet rice tea rotations (i.e., growing vanilla in soil previously planted with these crops) on Fusarium oxysporum abundance and rhizosphere microbial communities using real-time quantitative PCR and high-throughput sequencing.

RESULTS: Pandan rotation, in particular, reduced disease incidence to 17% and decreased F. oxysporum copy numbers; sweet rice tea showed similar suppressive effects. Crop rotation significantly increased fungal diversity and richness. Different cropping systems, including fallow, monoculture and crop rotation, significantly influenced fungal and bacterial community development, with cropping system and rotated crops being the main drivers of rhizosphere community assembly. The black pepper and pandan rotations specifically enriched certain fungal OTUs, such as OTU1_Thermomyces, OTU37_Arthrobotrys, and OTU18_Arthrobotrys, which serve as biomarkers for the presence of F. oxysporum. After pandan rotation, microbial interactions within the rhizosphere intensified, with notable enrichment of core bacterial taxa, including OTU22_Nitrosospira, OTU56_Lacibacterium, and OTU178_Actinospica. Soil pH was identified as a significant factor influencing microbial community assembly. The fungal community structure, along with core OTU22_Nitrosospira and soil pH, was pivotal in curbing pathogen growth, explaining 25.19%, 8.61%, and 20.45% of the variance, respectively.

CONCLUSION: This study revealed that incorporating pandan into crop rotation may effectively alleviate soil-borne diseases during vanilla production.},
}

@article {pmid40606160,
year = {2025},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Corrigendum: Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1639190},
doi = {10.3389/fmicb.2025.1639190},
pmid = {40606160},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1258775.].},
}

@article {pmid40606159,
year = {2025},
author = {Xiang, C and Su, L and Han, M and Liang, J and Hou, F and Liao, J},
title = {Comparative analysis of gut microbiota and metabolome in captive Chinese and Malayan pangolins.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1599588},
pmid = {40606159},
issn = {1664-302X},
abstract = {As an endangered species in the world, pangolins have attracted much attention due to their unique ecological value. In captivity, pangolins face numerous survival challenges, especially intestinal health problems, which are closely related to the gut microbiome and metabolome. The aim of this study was to contrast the gut microbiota and metabolome of Chinese pangolin and Malayan pangolin in captivity, which in order to explore the differences in digestive physiology and metabolic function between the two species. Through 16S rRNA gene sequencing and non-targeted metabolomics analysis, we identified significant differences in the composition and diversity of the gut microbiota between these two species. The gut microbiota of Chinese and Malayan pangolins is dominated by Firmicutes and Proteobacteria at phylum level. At the genus level, the abundance of Clostridium sensu stricto 13 in Chinese pangolins was significantly higher than Malayan pangolins, whereas Peptostreptococcus, and Blautia are more abundant in Malay pangolins. Moreover, integrative analysis of the microbiome and metabolome revealed important correlations: Peptostreptococcus was positively correlated with 13-HpOTrE (r) metabolism, while Clostridium sensu stricto 13 was negatively correlated with 13-HpOTrE (r) metabolism. Blautia was positively correlated with 1-phenylethylamine metabolism. These results provided important gut microbiome and metabolomics data for the conservation and artificial breeding of pangolins, which can help optimize captive pangolins feeding management and health maintenance.},
}

@article {pmid40606154,
year = {2025},
author = {Han, H and Fu, L and Wang, J and Sun, Y and Cao, D and Lei, Q and Zhou, Y and Li, F and Liu, W and Li, D and Hao, D and Liu, J},
title = {Effect of dietary supplementation with Brevibacillus laterosporus on broiler growth performance, meat quality and gut microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1608076},
pmid = {40606154},
issn = {1664-302X},
abstract = {This study aimed to investigate the effects of Brevibacillus laterosporus (B. laterosporus) supplementation on growth performance, carcass traits, antioxidant capacity, and cecal microbiota in broilers. A total of 320 one-day-old YS909 male broilers were randomly assigned to four dietary groups: control (CON), low-dose (LBL, 100 mg/kg), medium-dose (MBL, 300 mg/kg), and high-dose (HBL, 500 mg/kg) B. laterosporus supplementation (n = 8 replicates/group, 10 chicks/replicate). Growth performance, carcass traits, antioxidant capacity, and cecal microbiota/metabolites (MBL vs. CON) were analyzed. Dietary supplementation with B. laterosporus significantly decreased the feed intake / weight gain (F/G) in LBL (22-42 d and 1-42 d), MBL (22-42 d) and HBL (22-42 d) groups. Both MBL and HBL groups showed higher semi-eviscerated percentages than the control. The MBL group had a significantly increased eviscerated percentage. The LBL group had a significantly increased breast muscle percentage. Specifically, the HBL group exhibited a notable increase in muscle C18:3n3 content, and a significant decrease in muscle C18:1n9t and C20:3n3 content. The LBL group saw significant reductions in the proportion of C18:1n9t and C20:1. Additionally, the MBL group experienced significant decreases in the proportions of C18:3n3, C20:3n3 and C20:4n6. Dietary supplementation with B. laterosporus significantly enhanced the oxidative stress resistance of serum by decreasing malondialdehyde (MDA) levels and increasing glutathione peroxidase (GSH-PX) and total antioxidant capacity (T-AOC). 16S ribosomal DNA and metabolome sequencing of cecum contents was conducted for the MBL and CON groups. This analysis demonstrated significant increases in α-diversity indices in the MBL group. There was an increased relative abundance of Firmicutes and a decreased relative abundance of Bacteroidetes and Proteobacteria in the MBL group. In addition, the shifts of the cecal microbial community lead to the alteration of metabolites of the cecum including amino acid and lipid. In conclusion, dietary supplementation with medium-dose B. laterosporus enhanced broiler carcass traits and antioxidant status by modulating cecal microbiota and metabolites, demonstrating its potential as an effective feed additive.},
}

@article {pmid40606151,
year = {2025},
author = {Wang, C and Song, Z and Li, X and Liu, Q},
title = {Bacterial community shifts in Fusarium-induced avocado root rot and the antagonistic potential of Bacillus siamensis NB92.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626537},
pmid = {40606151},
issn = {1664-302X},
abstract = {Avocado root rot, driven by soil-borne fungi such as Fusarium spp., poses a major challenge to global avocado production. The rhizosphere microbiome is critical for plant health, yet the impact of root rot on bacterial community structure and its implications for disease management remain poorly understood. Here, we combined culture-independent 16S rDNA amplicon sequencing with culture-dependent isolation to characterize bacterial communities in healthy and Fusarium-infested avocado bulk and rhizosphere soils. Key beneficial taxa, notably Bacillus, were then isolated and evaluated for their antagonistic potential. Results showed that root rot significantly reduced rhizosphere bacterial α-diversity, altered community structure, and depleted phyla such as Actinobacteriota and Firmicutes that contain beneficial taxa. Beneficial genera such as Bacillus and Streptomyces declined, while cultivable Fusarium counts increased. Negative correlations between Fusarium abundance, the bacteria-to-fungi ratio, and the relative abundance of beneficial bacteria further underscore their suppressive role. Guided by these findings, we isolated Bacillus strain NB92, identified as Bacillus siamensis through morphological, biochemical, and 16S rRNA and gyrA gene analyses. NB92 exhibited strong antagonistic activity against the root rot pathogen (Fusarium sp. St7) via both direct antagonism and volatile organic compound production. Inoculating NB92 into diseased rhizosphere soil boosted Bacillus counts and reduced Fusarium abundance. Moreover, NB92 effectively inhibited the pathogen's necrotizing ability. B. siamensis NB92 thus represents a promising, sustainable biocontrol agent and contributes to the development of microbiome-based strategies for managing avocado root rot.},
}

@article {pmid40606147,
year = {2025},
author = {Guo, L and Wang, R and Han, L and Fu, Y and Wang, X and Nie, L and Fu, W and Ren, H and Wu, L and Li, G and Ding, J},
title = {Multi-omics integration identifies key biomarkers in retinopathy of prematurity through 16S rRNA sequencing and metabolomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1601292},
pmid = {40606147},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome is increasingly recognized for its role in the pathogenesis of neonatal conditions commonly associated with retinopathy of prematurity (ROP). This study aimed to identify key intestinal microbiota and metabolites in ROP and examine their relationships.

METHODS: Fecal samples were collected from infants with and without ROP at weeks 2 (T1) and 4 (T2) for 16S rRNA sequencing. At T2, additional fecal samples underwent non-targeted metabolomic analyses. A combined analysis of the 16S rRNA sequencing and metabolomics data was performed.

RESULTS: No significant differences in α-diversity indexes were observed between the ROP and non-ROP at T1. However, at T2, the Chao, ACE, and Shannon indices were significantly higher, whereas the Simpson index was lower in ROP compared to non-ROP. At the phylum level, the dominant phyla at T2 included Pseudomonadota, Bacillota, Actinomycetota, Bacteroidota, and Verrucomicrobiota. LEfSe analysis of T2 showed that Bifidobacterium, Rhodococcus, Staphyloococcus, Caulobacter, Sphingomonas, Aquabacterium, and Klebsiella as key genera associated with ROP. Metabolomic analysis identified 382 differentially accumulated metabolites, which were enriched in steroid hormone biosynthesis; the PPAR signaling pathway; linoleic acid metabolism; histidine metabolism; and alanine, aspartate, and glutamate metabolism. Additionally, the AUC of the combined analysis exceeded that of differential bacterial communities (0.9958) alone.

CONCLUSION: This study revealed characteristic changes in the intestinal flora and metabolites in ROP, which provide promising targets/pathways for ROP diagnosis and therapy.},
}

@article {pmid40606013,
year = {2025},
author = {Lee, J and Wu, HLA and Mannan, AA and Nakamura, Y and Amagai, M and Irvine, AD and Tanaka, RJ},
title = {Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.},
journal = {JID innovations : skin science from molecules to population health},
volume = {5},
number = {5},
pages = {100385},
pmid = {40606013},
issn = {2667-0267},
abstract = {Understanding how the skin microbiota contributes to skin health and disease requires knowledge of the dynamic interactions between the skin and its resident microbes. In silico modeling complements in vivo and in vitro experiments by enabling a systems-level understanding of dynamic skin-microbiota interactions. However, the number of published in silico skin microbiota models remains limited. This paper provides the first comprehensive exploration of in silico skin microbiota modeling. We identify current challenges, learn from leading experimental validation approaches adopted in in silico gut microbiota research, and propose ways to enhance the predictive power of in silico skin microbiota models.},
}

@article {pmid40605597,
year = {2025},
author = {Thomsen, L and Jacobsen, S and Tøttrup, A},
title = {[Pouchitis].},
journal = {Ugeskrift for laeger},
volume = {187},
number = {27},
pages = {},
doi = {10.61409/V01250033},
pmid = {40605597},
issn = {1603-6824},
mesh = {Humans ; *Pouchitis/drug therapy/diagnosis/etiology/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Proctocolectomy, Restorative/adverse effects ; Acute Disease ; Colitis, Ulcerative/surgery ; Chronic Disease ; },
abstract = {Pouchitis is the most common complication following ileal pouch-anal anastomosis. It is characterized by pouch inflammation and symptoms resembling ulcerative colitis. The aetiology is thought to involve a combination of genetic factors, a dysregulated immune response, and alterations in the gut microbiome. Pouchitis is classified as acute if symptoms less-than 4 weeks or chronic if symptoms > 4 weeks. Acute pouchitis is typically treated with antibiotics, while chronic pouchitis may require cyclic antibiotics or immunomodulatory therapy. This review indicates that more research is needed to improve understanding and treatment.},
}

Humans
*Pouchitis/drug therapy/diagnosis/etiology/therapy/microbiology
Anti-Bacterial Agents/therapeutic use
Proctocolectomy, Restorative/adverse effects
Acute Disease
Colitis, Ulcerative/surgery
Chronic Disease

@article {pmid40605535,
year = {2025},
author = {Xiang, X and Liu, H and Wang, T and Ding, P and Zhu, Y and Cheng, K and Ming, Y},
title = {Prediction of postoperative infection through early-stage salivary microbiota following kidney transplantation using machine learning techniques.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2519816},
doi = {10.1080/0886022X.2025.2519816},
pmid = {40605535},
issn = {1525-6049},
mesh = {Humans ; *Saliva/microbiology ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Machine Learning ; Adult ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Postoperative Complications/microbiology/diagnosis ; *Kidney Failure, Chronic/surgery ; Biomarkers/analysis ; },
abstract = {Kidney transplantation (KT) is an effective treatment for end-stage renal disease; however, the lifelong immunosuppressive regimen increases the risk of infection, presenting significant clinical, and economic challenges. Identifying predictive biomarkers for infection onset is critical. In this study, 122 postoperative saliva samples from 39 KT recipients were analyzed using 16S rRNA sequencing, with 16 developing infections within one year. The composition of the salivary microbiota differed significantly between the infection and control groups, with notable variations at the Phylum level. Infected patients exhibited higher alpha diversity and 12 dominant taxa. A random forest model, utilizing five-fold three-times repeated cross-validation and incorporating differential biomarkers, significantly outperformed baseline peripheral blood lymphocyte subpopulation (PBLS) counts in predicting infections (area under the curve, 85.97% ± 10.64% vs. 67.03% ± 15.54%, p = 0.0008). Stepwise logistic regression, integrating clinical data, PBLS counts, and microbiome information, identified Mogibacterium as a significant predictor. The relative abundance of Mogibacterium correlated significantly with the ratio of plateau PBLSs to baseline PBLSs. Early-stage salivary microbiota profiles were predictive of post-KT infections within one year, reflecting lymphocyte reconstitution dynamics.},
}

Humans
*Saliva/microbiology
*Kidney Transplantation/adverse effects
Male
Female
Middle Aged
*Machine Learning
Adult
RNA, Ribosomal, 16S/genetics
*Microbiota
*Postoperative Complications/microbiology/diagnosis
*Kidney Failure, Chronic/surgery
Biomarkers/analysis

@article {pmid40605344,
year = {2025},
author = {Kim, SM and Park, S and Ansari, A and Lee, G and Hur, YM and An, J and Lee, SS and You, YA and Kim, YJ},
title = {Altered Abundance of Butyrate-Producing Lachnospiraceae by Maternal Diet During Pregnancy Potentially Influences MASLD-Related Lipid Dysregulation in Male Rat Offspring.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70153},
doi = {10.1002/mnfr.70153},
pmid = {40605344},
issn = {1613-4133},
support = {NRF-2020R1I1A1A01071955//Basic Science Research Program through the National Research Foundation of Korea/ ; grantnumber//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; RS-2023-00248698//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; Young-AhYou//RP-Grant 2024 from Ewha Womans University/ ; NRF-5199990614253,EducationResearchCenterfor4IR-BasedHealthCare//BK21 FOUR (Fostering Outstanding Universities for Research) funded by the Ministry of Education(MOE, Korea) and National Research Foundation of Korea/ ; },
abstract = {The maternal diet during pregnancy is an important factor that influences the intrauterine environment during fetal development. However, the relationship among maternal diet, the gut microbiome of offspring, and health outcomes remains unclear. Here, we report that changes in the gut microbiome of offspring after maternal exposure to 50% food restriction and 45% high-fat diet during pregnancy can affect the risk of metabolic dysfunction-associated steatotic liver disease (MASLD) in offspring in a sex-specific manner. Notably, despite no significant difference in body weight, plasma triglyceride and leptin levels were significantly increased in male offspring compared with the controls. The relative abundance of the butyrate-producing genera of the Lachnospiraceae family was dependent on the sex of the offspring and correlated with plasma triglyceride and leptin levels. Interestingly, male offspring in the 50% restricted diet or 45% high-fat diet groups had reduced butyrate levels compared with the control group and were affected by oxidative damage and hepatic lipogenesis. Our findings suggest that the maternal diet during pregnancy affects the gut microbiota of male offspring in a sex-specific manner, potentially predisposing them to MASLD later in life through dysregulation of lipid metabolism.},
}

@article {pmid40605266,
year = {2025},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {A review of engraftment assessments following fecal microbiota transplant.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2525478},
doi = {10.1080/19490976.2025.2525478},
pmid = {40605266},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.},
}

*Fecal Microbiota Transplantation
Humans
*Gastrointestinal Microbiome
*Clostridium Infections/therapy/microbiology
Clostridioides difficile/physiology
Animals
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40605185,
year = {2025},
author = {Rather, RA},
title = {Shaping Plant Growth Beneath the Soil: A Theoretical Exploration of Fungal Endophyte's Role as Plant Growth-Promoting Agents.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70026},
pmid = {40605185},
issn = {2045-8827},
support = {//The author received no specific funding for this work./ ; },
mesh = {*Endophytes/physiology/metabolism ; *Soil Microbiology ; *Fungi/physiology/metabolism ; *Plant Development ; Soil/chemistry ; Symbiosis ; Plant Growth Regulators/metabolism ; *Plants/microbiology ; },
abstract = {Plant growth relies on both natural and agrochemical inputs, with natural soil nutrients and chemically synthesized fertilizers enhancing its growth. However, continuous fertilizer use can lead to soil alkalinity and environmental contamination, emphasizing the need for sustainable practices. Microbial agents, particularly fungal endophytes, have emerged as promising natural alternatives. They are recognized as integral components of the plant microbiome and aid in nutrient acquisition, hormone production, and stress resistance. Fungal endophytes enhance nutrient uptake by solubilizing phosphorus, fixing nitrogen, and producing siderophores that chelate iron. They also modulate plant hormones, including auxins, gibberellins, and cytokinins, promoting growth and development. Under abiotic stress, these endophytes improve plant tolerance by inducing systemic resistance and enhancing water and nutrient absorption. This review provides a comprehensive theoretical exploration of the role of fungal endophytes in promoting plant growth, examining their diversity, mechanisms of action, and practical applications. The focus is on understanding how these symbiotic organisms can be harnessed to enhance sustainable agricultural practices and contribute to environmental conservation.},
}

*Endophytes/physiology/metabolism
*Soil Microbiology
*Fungi/physiology/metabolism
*Plant Development
Soil/chemistry
Symbiosis
Plant Growth Regulators/metabolism
*Plants/microbiology

@article {pmid40605060,
year = {2025},
author = {Campanale, A and Siniscalco, D and Di Marzo, V},
title = {The endocannabinoidome-gut microbiome-brain axis as a novel therapeutic target for autism spectrum disorder.},
journal = {Journal of biomedical science},
volume = {32},
number = {1},
pages = {60},
pmid = {40605060},
issn = {1423-0127},
mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Endocannabinoids/metabolism ; *Autism Spectrum Disorder/drug therapy/microbiology/metabolism/physiopathology ; *Brain/metabolism ; Animals ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is characterized by disruption of the gut-brain axis, which leads to behavioral, psychiatric, metabolic and gastrointestinal symptoms. Effective ASD treatments are limited. Research highlights the roles of the endocannabinoidome (eCBome) and gut microbiome (GM), both crucial for brain and gut function. This review summarizes research on therapeutic targets within the eCBome-GM-brain axis for ASD and related comorbidities.

DISCUSSION: Evidence suggests that reduced levels of eCBome mediators, like oleoylethanolamide and anandamide, and altered cannabinoid type 1 and type 2 (CB1 and CB2) receptors activity may contribute to ASD symptoms, making them promising targets. Modulating the eCBome-GM-brain axis with inhibitors of fatty acid amide hydrolase (FAAH), transient receptor potential vanilloid 1, and monoacylglycerol lipase (MAGL) may improve repetitive, stereotypical, and sensory behaviors, and alleviate sociability impairments, depression and anxiety. However, inhibition of FAAH and MAGL may also induce ADHD-like behaviors, which can be reversed by CB1 inverse agonists. Targeting metabotropic glutamate receptor 5 to increase levels of the eCBome mediator 2-arachidonoylglycerol (2-AG) may benefit ASD-related behaviors. eCBome mediators such as 2-AG, 1/2-palmitoylglycerol and palmitoylethanolamide may also help manage ASD- and GI-related symptoms, and systemic inflammation. Other potential therapeutic targets that deserve further investigation are eCBome-related receptors G-protein-coupled receptor 55 and peroxisome proliferator-activated receptors-alpha and -gamma, and the cyclooxygenase-2/prostaglandin E2 pathway, which may address hyperactivity and repetitive behaviors. Additionally, mucin-degrading genera like Akkermansia and Ruminococcus may improve ASD-related GI symptoms such as hypersensitivity and inflammation. Selective antibiotics against specific Clostridium strains may improve irritability and aggression. In ASD with ADHD and OCD, treatments may involve modulating the CB1 and CB2 receptor, and bacterial families like Ruminococcaceae and Lachnospiraceae. Lastly, modulating the abundance of anti-inflammatory genera like Prevotella and Anaeroplasma, and taxa associated with gut health such as Roseburia may also offer therapeutic value.

CONCLUSION: The eCBome-GM-brain axis is a promising target for ASD treatment, meriting further clinical and preclinical research.},
}

*Gastrointestinal Microbiome/physiology/drug effects
Humans
*Endocannabinoids/metabolism
*Autism Spectrum Disorder/drug therapy/microbiology/metabolism/physiopathology
*Brain/metabolism
Animals

@article {pmid40605009,
year = {2025},
author = {Paix, B and Thivet, A and Domingos, C and Erol, Ö and van der Windt, N and Choi, YH and de Voogd, NJ},
title = {Adaptive strategies of Caribbean sponge holobionts beyond the mesophotic zone.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {157},
pmid = {40605009},
issn = {2049-2618},
support = {16.161.301//NWO-VIDI/ ; },
mesh = {Animals ; *Porifera/microbiology/physiology ; *Microbiota ; Caribbean Region ; Symbiosis ; Ecosystem ; Archaea/classification/genetics/metabolism/isolation & purification ; *Adaptation, Physiological ; Metabolome ; Bacteria/classification/genetics/metabolism/isolation & purification ; Nitrogen/metabolism ; },
abstract = {BACKGROUND: Marine sponges and their microbiomes function together as holobionts, playing essential roles in ecosystem dynamics and exhibiting remarkable adaptability across depth gradients. This study utilized a multi-omics approach, integrating microbiome and metabolome analyses, to investigate adaptive strategies in sponge holobionts inhabiting the mesophotic (80-125 m), upper-rariphotic (125-200 m), and lower-rariphotic (200-305 m) zones of Curaçao. We hypothesized that depth-related environmental factors drive distinct adaptive strategies, similar to patterns observed in fish and coral assemblages.

RESULTS: Results revealed major differences in holometabolomes and microbial communities between Demospongiae and Hexactinellida sponges, reflecting class-specific adaptive strategies. Notably, phospholipid homeoviscous adaptation to temperature and pressure might emerge as a key mechanism in phosphorus metabolism. Adaptations in nitrogen metabolism were linked to diverse ammonia oxidizing archaea (AOA) symbionts, and dissolved organic matter cycling. Hexactinellid microbiomes exhibited intra-specific heterogeneity; however, species-specific associations with AOA symbionts such as Cenarchaeum and Nitrosopumilus were observed. Additionally, the lower-rariphotic hexactinellid holometabolomes highlighted the significance of the nested ecosystem concept through the identification of secondary metabolites produced by their associated fauna (aphrocallistins by zoanthids and xanthurenic acid by shrimp).

CONCLUSIONS: This study highlights the ecological significance of sponge holobionts in mesophotic and rariphotic ecosystems, revealing diverse adaptations to unique physicochemical conditions and biotic interactions. Video Abstract.},
}

Animals
*Porifera/microbiology/physiology
*Microbiota
Caribbean Region
Symbiosis
Ecosystem
Archaea/classification/genetics/metabolism/isolation & purification
*Adaptation, Physiological
Metabolome
Bacteria/classification/genetics/metabolism/isolation & purification
Nitrogen/metabolism

@article {pmid40604917,
year = {2025},
author = {Chen, K and Qin, Y and Yan, L and Dong, Y and Lv, S and Xu, J and Kang, N and Luo, Z and Liu, Y and Pu, J and Chen, F and Jin, X},
title = {Variations in salivary microbiota and metabolic phenotype related to oral lichen planus with psychiatric symptoms.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {993},
pmid = {40604917},
issn = {1472-6831},
support = {82370968//the National Natural Science Foundations of China/ ; CSTB2022NSCQ-MSX1148//the Natural Science Foundation of Chongqing/ ; },
mesh = {Humans ; *Lichen Planus, Oral/microbiology/metabolism/psychology/complications ; *Saliva/microbiology/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Middle Aged ; Adult ; Case-Control Studies ; Phenotype ; Metabolome ; Depression/complications ; },
abstract = {BACKGROUND: Oral lichen planus (OLP) is a common chronic inflammatory disease of the oral mucosa with a certain tendency for malignant transformation. The etiology and pathogenesis of OLP remain unclear, and the relationship between psychiatric factors and the development of OLP has attracted much attention in recent years. This study aims to investigate the alterations in oral microbiota and metabolites in OLP patients with psychiatric symptoms, providing a theoretical foundation for understanding the pathogenesis and treatment of OLP.

METHODS: 16S rRNA sequencing was used to evaluate the oral microbial population in a cohort of 105 OLP patients. To further investigate the potential interaction between OLP and psychiatric factors, saliva samples from 64 depressed/anxious OLP patients (D-OLP) and their age-matched healthy controls were selected for 16S rRNA sequencing. The salivary metabolome was also characterized by ultra performance liquid chromatography-mass spectrometry (LC-MS).

RESULTS: The results of 16S rRNA sequencing showed that significant differences in species classification between OLP patients and healthy controls. The D-OLP group displayed an increased abundance of Pseudomonas as well as dysregulation of associated metabolism activities. Correlation analysis showed that the altered metabolites were involved in the metabolic pathways related to the oral-microbiome-brain axis and affected various physiological processes such as neurotransmitter transmission and oxidative stress, promoting epithelial inflammatory activation and immune responses. These changes ultimately lead to the destruction of the original oral mucosal homeostasis.

CONCLUSIONS: Psychiatric factors may promote mucosal inflammatory responses through dysbiosis of the microbiota. The dysregulated oral microbiome-related metabolites may significantly affect the pathogenesis of the oral-brain axis in OLP patients.This study provides valuable insights into potential future modalities for elucidating the pathogenesis of OLP, offering a foundation for the development of personalized therapeutic strategies.},
}

Humans
*Lichen Planus, Oral/microbiology/metabolism/psychology/complications
*Saliva/microbiology/metabolism
Male
Female
RNA, Ribosomal, 16S/genetics
*Microbiota
Middle Aged
Adult
Case-Control Studies
Phenotype
Metabolome
Depression/complications

@article {pmid40604910,
year = {2025},
author = {You, Y and Wu, HL and Chen, DY and Yu, SY and Xu, Y and Tang, Y and Sun, HL and Huang, C},
title = {Human calculus adhesive-induced periodontitis model recapitulating human periodontitis microbiota in rats.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1034},
pmid = {40604910},
issn = {1472-6831},
support = {81970918//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Periodontitis/microbiology/pathology ; Humans ; *Disease Models, Animal ; Rats ; *Microbiota ; *Dental Calculus/microbiology ; Alveolar Bone Loss/microbiology ; Porphyromonas gingivalis ; Male ; X-Ray Microtomography ; Rats, Sprague-Dawley ; Fusobacterium nucleatum/isolation & purification ; Gingiva/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory condition characterized by oral dysbiosis. Current animal models of periodontitis using ligation and pathogen inoculation are time-consuming and do not reflect the chronic characteristics of human periodontitis. One of the significant differences is the difference between the current experimental animal periodontitis microbiome and human periodontitis microbiome. This study aims to establish a humanized rat model that mimics clinical conditions and approximates the microbial causes of human periodontitis.

METHODS: The human calculus adhesive-induced periodontitis (hCAP) was established by transplanting subgingival dental calculus from periodontitis patients to the subgingival surface of rats using universal adhesive. The study performed stereomicroscopy, micro-CT analysis, hematoxylin and eosin staining, tartrate-resistant acid phosphatase staining, qRT-PCR, ELISA, and 16s rDNA sequencing.

RESULTS: The hCAP group showed significant alveolar bone loss and osteoclast formation. The inflammatory factors in gingiva and serum were dramatically increased compared to the placebo rats, revealed by qRT-PCR and ELISA. The oral microbiota of the hCAP group was found to be more similar to that of patients compared with ligation with Porphyromonas gingivalis model, with enhanced colonization of Fusobacterium nucleatum subsp. polymorphum and Prevotella intermedia. The hCAP model also detected pathogenic bacteria of systemic diseases as shown in 16s rDNA sequencing.

CONCLUSIONS: The hCAP model mimics clinical conditions, approximates the microbial causes of human periodontitis and preserve bacteria responsible for systemic diseases in the gingival area of rats. The hCAP model may help in understanding the association between periodontitis and systemic diseases.},
}

Animals
*Periodontitis/microbiology/pathology
Humans
*Disease Models, Animal
Rats
*Microbiota
*Dental Calculus/microbiology
Alveolar Bone Loss/microbiology
Porphyromonas gingivalis
Male
X-Ray Microtomography
Rats, Sprague-Dawley
Fusobacterium nucleatum/isolation & purification
Gingiva/microbiology
RNA, Ribosomal, 16S

@article {pmid40604909,
year = {2025},
author = {Wang, J and Liu, Z and Wang, X and Zhang, Z and Zhou, T and Li, M and Wang, S and Hu, Z and Sun, R and Li, D},
title = {Combatting glufosinate-induced pepper toxicity: jasmonic acid recruiting rhizosphere bacterial strain Rhodococcus gordoniae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {158},
pmid = {40604909},
issn = {2049-2618},
support = {22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 22067004//National Nature Science Foundation of China/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; 321CXTD436//Natural Science Foundation of Hainan Province/ ; },
mesh = {*Rhizosphere ; *Oxylipins/metabolism/pharmacology ; Soil Microbiology ; *Cyclopentanes/metabolism/pharmacology ; *Rhodococcus/metabolism/drug effects/isolation & purification/genetics/growth & development/classification ; *Capsicum/drug effects/microbiology/growth & development ; Plant Roots/microbiology ; *Aminobutyrates/toxicity/metabolism ; Biodegradation, Environmental ; Caffeic Acids/pharmacology ; Microbiota ; },
abstract = {BACKGROUND: Plant-microbe interactions are essential for mitigating abiotic and biotic stressors by shaping the rhizosphere environment. However, how rhizosphere beneficial bacteria and plant metabolites respond to glufosinate (GLU)-induced toxicity remains largely unknown.

RESULTS: Our study investigates the impact of GLU on chili plant growth and rhizosphere microbiome, emphasizing GLU-induced alterations in amino acid profiles, secondary metabolites, and microbial community composition, with notable enrichment of the Rhodococcus genus. To uncover the underlying mechanisms of Rhodococcus genus-root exudate interactions under GLU stress, we successfully isolated an efficient Rhodococcus gordoniae strain TR-5 from soil samples contaminated with GLU. This strain, isolated from GLU-contaminated soil, demonstrates potential for bioremediation and achieved over 95% GLU degradation efficiency at 35 °C, pH 6.38, and 1% inoculation rate. Through growth analysis, chemotaxis analysis, and molecular docking, caffeic acid disrupts the bacterial strain's metabolic pathways and impedes TR-5 development. In contrast, jasmonic acid (JA) acts as a chemoattractant, promoting bacterial growth and metabolic activity to degrade GLU residues, thereby effectively degrading GLU residues in the soil.

CONCLUSIONS: This research indicates that GLU significantly influences the metabolic mechanisms of pepper plants. The optimization of microbial remediation strategies may improve soil remediation efficiency and reduce environmental impacts, highlighting opportunities for integrating microbial remediation into sustainable agricultural practices. Our findings provide insights into the role of JA in attracting and promoting the growth and metabolic activities of the Rhodococcus genus, which could be harnessed to improve soil remediation and plant health under GLU stress. Video Abstract.},
}

*Rhizosphere
*Oxylipins/metabolism/pharmacology
Soil Microbiology
*Cyclopentanes/metabolism/pharmacology
*Rhodococcus/metabolism/drug effects/isolation & purification/genetics/growth & development/classification
*Capsicum/drug effects/microbiology/growth & development
Plant Roots/microbiology
*Aminobutyrates/toxicity/metabolism
Biodegradation, Environmental
Caffeic Acids/pharmacology
Microbiota

@article {pmid40604874,
year = {2025},
author = {Zhou, X and Zheng, W and Kong, W and Zeng, T},
title = {Identification of circulating inflammation cytokines as a mediator of gut microbiota and type 2 diabetes mellitus: a Mendelian randomization study.},
journal = {Diabetology & metabolic syndrome},
volume = {17},
number = {1},
pages = {249},
pmid = {40604874},
issn = {1758-5996},
support = {82270909//National Natural Science Foundation of China/ ; 2020BCB003//Key R&D Program of Hubei Province/ ; },
abstract = {BACKGROUND: Several studies have suggested that the gut microbiota (GM) may be associated with type 2 diabetes mellitus (T2DM). However, the causal relationship between GM and T2DM and whether inflammatory cytokines act as mediators remain unclear.

AIMS: To investigate the association between GM and T2DM and the proportion of this association that is mediated through inflammatory cytokines.

METHODS: We conducted a bidirectional and mediation Mendelian randomization (MR) study utilizing data from the genome-wide association studies (GWAS) of four sources of GM taxa (MiBioGen consortium, n = 18,340; Dutch Microbiome Project, n = 7,738; German biobanks, n = 8,956; FINRISK 2002, n = 5,959), a meta-analysis of inflammatory proteins (n = 14,824), and European-ancestry T2DM (n = 1,528,967). The inverse variance weighted method was applied as the primary method. And two-step MR was employed to identify potential mediating inflammatory cytokines.

RESULTS: We found evidence for 28 positive and 20 negative causal effects between multiple sources of GM and T2DM using at least two MR methods. And there were 2 positive and 5 negative causal relationships between cytokines and T2DM using at least two MR methods. The mediation MR analysis found that interferon-gamma (IFN-γ) mediated the causal effects of species Kandleria vitulina on T2DM (proportion mediated = 22.5%, P = 0.022).

CONCLUSION: The MR study supports the causal effect between Kandleria vitulina species and T2DM, with a potential mediating role played by inflammatory factor IFN-γ. Such result would serve as evidence for GM-targeted and cytokine-targeted therapy to prevent T2DM.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13098-025-01792-8.},
}

@article {pmid40604730,
year = {2025},
author = {Immonen, E and Paulamäki, L and Piippo, H and Nikkilä, A and Aine, L and Peltomäki, T and Lohi, O and Parikka, M},
title = {Oral microbiome diversity and composition before and after chemotherapy treatment in pediatric oncology patients.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {981},
pmid = {40604730},
issn = {1472-6831},
mesh = {Humans ; Child ; *Microbiota/drug effects ; *Stomatitis/microbiology/chemically induced/prevention & control ; Adolescent ; Male ; Female ; Double-Blind Method ; Child, Preschool ; *Neoplasms/drug therapy ; *Antineoplastic Agents/adverse effects/therapeutic use ; RNA, Ribosomal, 16S ; Mouthwashes/therapeutic use ; Mouth Mucosa/microbiology ; },
abstract = {OBJECTIVE: This study investigated the impact of anticancer treatment on the oral microbiome in pediatric patients and its association with oral mucositis (OM).

MATERIALS AND METHODS: A double-blind, randomized trial involving 34 pediatric cancer patients (ages 2-17.99) with solid or hematological malignancies. Mucosal swab samples were collected before and after chemotherapy. Patients underwent two 7-day rinse cycles-one with Caphosol and one with saline-in a randomized order. Bacterial DNA from 110 mucosal swabs was analyzed using 16S rRNA sequencing.

RESULTS: Chemotherapy altered bacterial composition. No life-threatening OM cases (WHO grade 4) were observed, but mild to severe OM (grades 1-3) occurred in three patients. In patients without oral lesions, Bergeyella genus was more abundant prior to treatment while Alloprevotella was more abundant in the post-treatment samples, compared to patients with lesions. OM was linked to distinct microbiome profiles, including Stenotrophomonas, Leptotrichia sp., Serratia sp.,Capnocytophaga sputigena, Sphingomonas sp., Parapusillimonas sp., Staphylococcus sp., and Turicibacter genera. Additionally, Burkholderia-Caballeronia-Paraburkholderia (p = 0.013) were more prevalent in the Caphosol group compared to the saline group.

CONCLUSIONS: These findings indicate that chemotherapy-induced microbiome shifts associate with OM risk, highlighting the potential for microbial markers to predict high-risk patients and support protective strategies.

TRIAL REGISTRATION: The trial titled "Supersaturated Calcium Phosphate Oral Rinse (Caphosol®) for the Prevention of Oral Mucositis in Children Undergoing Chemotherapeutic Treatments" was registered on ClinicalTrials.gov (ID NCT02807337), with the first submission date 2016-06-07.},
}

Humans
Child
*Microbiota/drug effects
*Stomatitis/microbiology/chemically induced/prevention & control
Adolescent
Male
Female
Double-Blind Method
Child, Preschool
*Neoplasms/drug therapy
*Antineoplastic Agents/adverse effects/therapeutic use
RNA, Ribosomal, 16S
Mouthwashes/therapeutic use
Mouth Mucosa/microbiology

@article {pmid40604405,
year = {2025},
author = {Jing, D and Jiang, X and Ren, X and Hao, R and Su, J and Li, X},
title = {Clinical performance of nanopore targeted sequencing for diagnosing endophthalmitis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {403},
pmid = {40604405},
issn = {1471-2180},
support = {ZR2024QH310//Shandong Provincial Natural Science Foundation/ ; BYSYZD2021044//Peking University Third Hospital Key Talent Project foundation/ ; },
mesh = {Humans ; *Endophthalmitis/diagnosis/microbiology ; *Bacteria/genetics/isolation & purification/classification ; Male ; *Nanopore Sequencing/methods ; Female ; Middle Aged ; Aqueous Humor/microbiology ; Aged ; Vitreous Body/microbiology ; Fungi/genetics/isolation & purification/classification ; Adult ; },
abstract = {PURPOSE: Rapid identification of pathogenic bacteria in the vitreous and/or aqueous humor of patients with acute clinical diagnosis of endophthalmitis via nanopore sequencing technology.

METHODS: We recruited a total of 12 patients (12 eyes) who were diagnosed with endophthalmitis at an ophthalmic outpatient clinic of Peking University Third Hospital from January 2022 to October 2022. Clinical evaluation is conducted in the order of consultation, symptom evaluation, physical sign evaluation, and ophthalmic special examination, all of which are completed by the same experienced clinical physician. Finally, 19 aqueous humor and/or vitreous samples were obtained via anterior chamber wash, vitreous tap and vitrectomy. The samples were separated for cultivation, biochemical drug sensitivity identification, and targeted nanopore sequencing (NTS), and the results of nanopore sequencing were validated via Sanger sequencing.

RESULTS: In patients with endophthalmitis, NTS can identify infected pathogens within 8-12 h. Six samples (31.6%) were subjected to culture-based diagnosis, while NTS revealed the presence of pathogenic microorganisms in 19 samples (100%), of which bacteria and fungi were detected in three samples. A total of 19 samples were subjected to Sanger sequencing, of which 16 (84.2%) tested positive, including 6 culture-positive samples and 10 culture-negative samples, of which 5 (26.3%) were positive for two bacterial genera. In culture-positive cases, there is a high-quality match between culture and targeted nanopore sequencing.

CONCLUSIONS: NTS can quickly detect pathogenic bacteria in samples from patients with endophthalmitis. Moreover, the use of vitreous and/or aqueous humor for the NTS has potential. NTS is a promising diagnostic platform for endophthalmitis, especially for mixed infections and culture-negative cases.},
}

Humans
*Endophthalmitis/diagnosis/microbiology
*Bacteria/genetics/isolation & purification/classification
Male
*Nanopore Sequencing/methods
Female
Middle Aged
Aqueous Humor/microbiology
Aged
Vitreous Body/microbiology
Fungi/genetics/isolation & purification/classification
Adult

@article {pmid40604391,
year = {2025},
author = {Djondji Kamga, FM and Jean Mugenzi, LM and Ngannang-Fezeu, VB and Ngambia Freitas, FS and Bouaka Tsakeng, CU and Sandeu, MM and Tchouakui, M and Wondji, CS},
title = {Evidence of microbiome contribution to the escalation of pyrethroid resistance in the major malaria vectors Anopheles gambiae s.s. and Anopheles funestus s.s.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {384},
pmid = {40604391},
issn = {1471-2180},
support = {217188/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Anopheles/microbiology/drug effects ; *Pyrethrins/pharmacology ; *Insecticide Resistance/genetics ; *Mosquito Vectors/microbiology/drug effects ; *Insecticides/pharmacology ; *Microbiota/drug effects ; Malaria/transmission ; *Bacteria/genetics/classification/drug effects/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Exacerbation of pyrethroid resistance severely jeopardises the effectiveness of malaria vector control efforts. However, the mechanisms enabling the vectors to now survive exposure to very high doses of pyrethroids remain unclear. Here, using High-throughput sequencing of the 16 S ribosomal RNA gene coupled with antibiotic treatment, we provide evidence linking the mosquito microbiome to the escalation of pyrethroid resistance in major African malaria vectors, Anopheles gambiae (s.s.) and Anopheles funestus (s.s.).

RESULTS: Phenotypic characterisation of An. gambiae (s.s.) and An. funestus (s.s.) populations revealed a high level of resistance to pyrethroid in both species, with mortality rates < 91% at 10x the diagnostic dose of each insecticide. A significant difference in bacterial composition was observed in An. gambiae s.s. between resistant mosquitoes exposed to 1X and 10X the diagnostic dose of permethrin, and the susceptible strains (PERMANOVA-F: 8.06; p = 0.02). The abundance of Pseudomonas_1 (Log2FC: 4.42, p = 0.0001) and Burkholderia_1 (Log2FC: 4.95, p = 0.001) bacteria were consistently associated with mosquitoes surviving 1X and 10X the diagnostic concentrations of permethrin, respectively, while Serratia_2 bacteria was mostly associated with insecticide susceptibility. In the An. funestus s.s. strain, there was no significant difference in bacterial alpha- and beta-diversity between the FUMOZ-R (exhibiting normal deltamethrin resistance) and FUMOZ-HR (selected for high deltamethrin resistance), suggesting a minimal impact of selection pressure on bacterial composition. However, in FUMOZ-HR, there was an increase in the abundance of Rahnella (Log2FC: 15.954, p = 9.73 E-12) and Leucobacter (Log2FC: 7.6, p = 0.008) bacteria, indicating their potential role in worsening deltamethrin resistance. Furthermore, treating resistant mosquitoes (both Anopheles species) with broad-spectrum bactericidal antibiotics (penicillin/streptomycin) via sugar solution increased their susceptibility to various diagnostic doses of permethrin and deltamethrin in WHO pyrethroid intensity bioassays.

CONCLUSION: Overall, our study emphasises the potential role of the microbiome in the escalation of insecticide resistance in Anopheles mosquitoes, identifying key bacterial strains associated with insecticide resistance and susceptibility. These candidate bacteria warrant further investigation to elucidate the mechanisms by which they contribute to the escalation of pyrethroid resistance.},
}

Animals
*Anopheles/microbiology/drug effects
*Pyrethrins/pharmacology
*Insecticide Resistance/genetics
*Mosquito Vectors/microbiology/drug effects
*Insecticides/pharmacology
*Microbiota/drug effects
Malaria/transmission
*Bacteria/genetics/classification/drug effects/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
High-Throughput Nucleotide Sequencing

@article {pmid40604389,
year = {2025},
author = {Yang, J and Wang, L and Liang, Q and Wang, Y and Yang, X and Wu, X and Pei, X},
title = {Microbiome, resistome, and potential transfer of antibiotic resistance genes in Chinese wet market under One Health sectors.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {406},
pmid = {40604389},
issn = {1471-2180},
support = {TB2024045//Special Funding for Postdoctoral Research Projects in Sichuan Province/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; 2022ZDZX0017//Department of Science and Technology of Sichuan Province (Major Science and Technology Projects)/ ; },
abstract = {BACKGROUND: Antibiotic resistance has become a serious challenge to global public health. The spread of antibiotic resistance genes (ARGs) among humans, animals, and the environment has become a critical issue within the “One Health” framework. Chinese wet market with live poultry trade provides an interface for close interaction between humans and chickens, and is considered as potential source for disease dissemination. However, the understanding of ARGs in this kind of market, including their shared profiles, influencing factors, and potential horizontal transfer subtypes and directions, remains limited.

RESULTS: In this study, we explored the microbiome, resistome, and mobility of ARGs, and identified putative horizontal gene transfer (HGT) events in the Chinese wet market system by utilizing metagenomic assembly and binning. Consequently, a total of 1080 ARG subtypes were identified from 36 metagenomes, and 221 subtypes were shared among human feces, chicken feces, chicken carcasses, and the environment. The composition of ARGs was influenced by mobile genetic elements (MGEs) and bacterial communities. As for the host of ARGs, 89 ARG-carrying genomes (ACGs) were identified, with 18 of them carrying multiple ARGs and MGEs, indicating the potential mobility of ARGs. Notably, six ACGs were identified as opportunistic pathogens carrying multiple ARGs and MGEs, which were annotated as Escherichia coli, Acinetobacter johnsonii, Klebsiella variicola, Klebsiella pneumoniae, and Citrobacter freundii. In addition, 164 potential HGT events were identified based on ACGs, and ParS, vanB, ugd, and macB were annotated as potentially transferred ARG subtypes in humans and the wet market.

CONCLUSIONS: This study offers new insights into the potential for HGT of ARGs within a Chinese wet market setting, highlighting putative transmission patterns among humans, poultry, and the environment. To our knowledge, few studies have explored ARG transfer potential in this context using metagenome-assembled genomes, making this a valuable contribution to One Health surveillance.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04115-z.},
}

@article {pmid40604388,
year = {2025},
author = {Han, D and Zhang, Y and Liu, W and Wan, R and Hu, J and Pan, F and Pan, X and Weng, W and Wang, Y and Ma, Z and Zhang, H and Chen, J},
title = {Disruption of gut microbiome and metabolome in treatment-naïve children with attention deficit hyperactivity disorder.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {381},
pmid = {40604388},
issn = {1471-2180},
support = {21ZR1452900//Natural Science Foundation of Shanghai/ ; 19ZR1477700//Natural Science Foundation of Shanghai/ ; 82471882//National Natural Science Foundation of China/ ; shslczdzk06902//Shanghai Municipal Key Clinical Specialty/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; 2022YFC2705203//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Child ; *Metabolome ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder with an increasing prevalence in children. Recent studies have suggested that the gut microbiota may play a significant role in the development of ADHD. However, the specific relationship between changes in intestinal bacteria and related metabolites in children with ADHD remains poorly understood.

RESULTS: In this study, we illustrated the fecal microbiome, metabolome and lipidome, as well as plasma metabolome using 16S rRNA gene sequencing and LC-MS in 15 pairs of children with ADHD and healthy controls. Our results revealed imbalance of gut microbiota and dysregulation of metabolites in individuals with ADHD. Specifically, children with ADHD exhibited significantly lower abundance of the Actinobacteria phylum, particularly Bifidobacterium, Corynebacterium and Actinomyces, while Veillonella in the Negativicutes class showed significant high level. No children with ADHD were classified under enterotype 1, which was composed solely of healthy children. Integration of multi-omics data suggested that the Bifidobacterium genus, which is positively correlated with various neurotransmitter precursor amino acid metabolites, may contribute to ADHD by downregulating pathways involving dopaminergic, serotonergic and glutamatergic systems.

CONCLUSIONS: These findings highlight the crucial regulatory impact of gut microbiota in the development of ADHD through metabolic pathways, and provide a potential avenue to the diagnosis and intervention of ADHD.},
}

Humans
*Gastrointestinal Microbiome
*Attention Deficit Disorder with Hyperactivity/microbiology/metabolism
Child
*Metabolome
Male
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Female
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40604383,
year = {2025},
author = {Yao, C and Yang, Y and Qiu, M and Jin, D and Huang, J},
title = {The effect of Akkermansia in patients with pregnancy induced hypertension.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {386},
pmid = {40604383},
issn = {1471-2180},
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Adult ; *Hypertension, Pregnancy-Induced/microbiology/blood ; Case-Control Studies ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Cytokines/blood ; Follow-Up Studies ; Biomarkers/blood ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUNDS: Intestinal dysbiosis in the second trimester is associated with pregnancy-induced hypertension (PIH) in the first trimester. However, the consequences and underlying mechanisms remain unclear.

METHODS: In a follow-up cohort study, a nested case-control design was employed. Twenty healthy pregnant women in their second trimester were selected as controls, while nineteen patients with pregnancy-induced hypertension were included in the study. The 16 S rRNA sequencing was utilized to assess changes of gut microbiota patterns during early pregnancy. ELISA test was used to measure plasma inflammatory markers such as IL-1 beta, IL-6, TNF alpha, IL-8 and IL-10.

RESULTS: The PIH group exhibited lower microbial α-diversity compared to the healthy group. Although no statistically significant difference was observed at the genus level (p = 0.05), at the phylum level, the PIH patients showed a reduced abundance of Verrucomicrobia and an increased abundance of Firmicutes (p = 0.011). Donis analysis revealed that the Gut Microbiome Health Index (GMHI) of the PIH group was significantly worse than that of the control group. Additionally, Akkermansia abundance was significantly lower in the PIH group compared to the control group. Furthermore, more pro-inflammatory cytokines, such as IL-18 and capase-1, were produced in PIH plasma compared to the control group.

CONCLUSION: The correlation analysis between gut microbiota and cytokines in PIH patients and controls revealed that Akkermansia was positively associated with IL-18 and capase-1 levels in PIH patients.},
}

Humans
Female
Pregnancy
*Gastrointestinal Microbiome
Adult
*Hypertension, Pregnancy-Induced/microbiology/blood
Case-Control Studies
*Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Cytokines/blood
Follow-Up Studies
Biomarkers/blood
Bacteria/classification/genetics/isolation & purification