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ESP: PubMed Auto Bibliography 18 Feb 2025 at 01:53 Created:
Microbiome
It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.
Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion
Citations The Papers (from PubMed®)
RevDate: 2025-02-17
The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.
Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association [Epub ahead of print].
BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.
METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.
RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.
CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.
Additional Links: PMID-39961991
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@article {pmid39961991,
year = {2025},
author = {Booth, ME and Wood, HM and Travis, MA and , and Quirke, P and Grabsch, HI},
title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {},
number = {},
pages = {},
pmid = {39961991},
issn = {1436-3305},
abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.
METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.
RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.
CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Integrating alternative therapies in overcoming chemotherapy resistance in tumors.
Molecular biology reports, 52(1):239.
Chemotherapy-resistant tumors present a significant challenge in oncology, often leading to treatment failures owing to mechanisms such as genetic mutations, drug efflux, altered metabolism, and adaptations within the tumor microenvironment. These factors limit the effectiveness of treatment and contribute to tumor resistance. This review highlights the role of alternative therapies aimed at overcoming resistance mechanisms. Several alternative strategies with high efficacy rate against tumor resistance are being explored, including targeted therapies (58-64%), immunotherapy (80%), hormone therapy (22-61%), and emerging approaches such as herbal therapies (90%), probiotics (34-90%), metabolic therapies (> 50%), epigenetic therapies (51-89%), microbiome-based therapies (50%), gene therapy (67-80%), photodynamic therapy/hypothermia (86-99%), and nanotechnology (50-67%). Integrating these alternative strategies with conventional treatments has the potent-al to augment the therapeutic efficacy and patient outcomes. Despite this progress, limitations in cancer therapeutics include the lack of predictive biomarkers, resistance mechanisms, and tumor heterogeneity, all of which contribute to treatment failure and relapse. To address these limitations, advancements in molecular diagnostics, as well as early detection through liquid biopsies, and the use of biomarkers to monitor resistance and guide treatment are crucial. Additionally, expanding clinical trials is essential to validate new therapies and improve patient outcomes.
Additional Links: PMID-39961936
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@article {pmid39961936,
year = {2025},
author = {Alqarni, SS and Khan, NU},
title = {Integrating alternative therapies in overcoming chemotherapy resistance in tumors.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {239},
pmid = {39961936},
issn = {1573-4978},
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; *Neoplasms/drug therapy/therapy/genetics ; *Complementary Therapies/methods ; Tumor Microenvironment/drug effects ; Antineoplastic Agents/therapeutic use/pharmacology ; Immunotherapy/methods ; },
abstract = {Chemotherapy-resistant tumors present a significant challenge in oncology, often leading to treatment failures owing to mechanisms such as genetic mutations, drug efflux, altered metabolism, and adaptations within the tumor microenvironment. These factors limit the effectiveness of treatment and contribute to tumor resistance. This review highlights the role of alternative therapies aimed at overcoming resistance mechanisms. Several alternative strategies with high efficacy rate against tumor resistance are being explored, including targeted therapies (58-64%), immunotherapy (80%), hormone therapy (22-61%), and emerging approaches such as herbal therapies (90%), probiotics (34-90%), metabolic therapies (> 50%), epigenetic therapies (51-89%), microbiome-based therapies (50%), gene therapy (67-80%), photodynamic therapy/hypothermia (86-99%), and nanotechnology (50-67%). Integrating these alternative strategies with conventional treatments has the potent-al to augment the therapeutic efficacy and patient outcomes. Despite this progress, limitations in cancer therapeutics include the lack of predictive biomarkers, resistance mechanisms, and tumor heterogeneity, all of which contribute to treatment failure and relapse. To address these limitations, advancements in molecular diagnostics, as well as early detection through liquid biopsies, and the use of biomarkers to monitor resistance and guide treatment are crucial. Additionally, expanding clinical trials is essential to validate new therapies and improve patient outcomes.},
}
MeSH Terms:
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Humans
*Drug Resistance, Neoplasm/genetics
*Neoplasms/drug therapy/therapy/genetics
*Complementary Therapies/methods
Tumor Microenvironment/drug effects
Antineoplastic Agents/therapeutic use/pharmacology
Immunotherapy/methods
RevDate: 2025-02-17
CAZyme3D: a database of 3D structures for carbohydrate-active enzymes.
Journal of molecular biology pii:S0022-2836(25)00067-1 [Epub ahead of print].
CAZymes (Carbohydrate Active EnZymes) degrade, synthesize, and modify all complex carbohydrates on Earth. CAZymes are extremely important to research in human health, nutrition, gut microbiome, bioenergy, plant disease, and global carbon recycling. Current CAZyme annotation tools are all based on sequence similarity. A more powerful approach is to detect protein structural similarity between query proteins and known CAZymes indicative of distant homology. Here, we developed CAZyme3D (https://pro.unl.edu/CAZyme3D/) to fill the research gap that no dedicated 3D structure databases are currently available for CAZymes. CAZyme3D contains a total of 870,740 AlphaFold predicted 3D structures (named Whole dataset). A subset of CAZymes 3D structures from 188,574 nonredundant sequences (named ID50 dataset) were subject to structural similarity-based clustering analyses. Such clustering allowed us to organize all CAZyme structures using a hierarchical classification, which includes existing levels defined by the CAZy database (class, clan, family, subfamily) and newly defined levels (subclasses, structural cluster [SC] groups, and SCs). The inter-family structural clustering successfully grouped CAZy families and clans with the same structural folds in the same subclasses. The intra-family structural clustering classified structurally similar CAZymes into SCs, which were further classified into SC groups. SCs and SC groups differed from sequence similarity-based CAZy subfamilies. With CAZyme structures as the search database, we created job submission pages, where users can submit query protein sequences or PDB structures for a structural similarity search. CAZyme3D will be a useful new tool to assist the discovery of novel CAZymes by providing a comprehensive database of CAZyme 3D structures.
Additional Links: PMID-39961523
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@article {pmid39961523,
year = {2025},
author = {Shanmugam, NRS and Yin, Y},
title = {CAZyme3D: a database of 3D structures for carbohydrate-active enzymes.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169001},
doi = {10.1016/j.jmb.2025.169001},
pmid = {39961523},
issn = {1089-8638},
abstract = {CAZymes (Carbohydrate Active EnZymes) degrade, synthesize, and modify all complex carbohydrates on Earth. CAZymes are extremely important to research in human health, nutrition, gut microbiome, bioenergy, plant disease, and global carbon recycling. Current CAZyme annotation tools are all based on sequence similarity. A more powerful approach is to detect protein structural similarity between query proteins and known CAZymes indicative of distant homology. Here, we developed CAZyme3D (https://pro.unl.edu/CAZyme3D/) to fill the research gap that no dedicated 3D structure databases are currently available for CAZymes. CAZyme3D contains a total of 870,740 AlphaFold predicted 3D structures (named Whole dataset). A subset of CAZymes 3D structures from 188,574 nonredundant sequences (named ID50 dataset) were subject to structural similarity-based clustering analyses. Such clustering allowed us to organize all CAZyme structures using a hierarchical classification, which includes existing levels defined by the CAZy database (class, clan, family, subfamily) and newly defined levels (subclasses, structural cluster [SC] groups, and SCs). The inter-family structural clustering successfully grouped CAZy families and clans with the same structural folds in the same subclasses. The intra-family structural clustering classified structurally similar CAZymes into SCs, which were further classified into SC groups. SCs and SC groups differed from sequence similarity-based CAZy subfamilies. With CAZyme structures as the search database, we created job submission pages, where users can submit query protein sequences or PDB structures for a structural similarity search. CAZyme3D will be a useful new tool to assist the discovery of novel CAZymes by providing a comprehensive database of CAZyme 3D structures.},
}
RevDate: 2025-02-17
Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.
Applied biochemistry and biotechnology [Epub ahead of print].
Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.
Additional Links: PMID-39961944
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@article {pmid39961944,
year = {2025},
author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A},
title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39961944},
issn = {1559-0291},
support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.},
}
RevDate: 2025-02-17
Gut microbiota-related neuroinflammation at the crossroad of food reward alterations: implications for eating disorders.
Gut pii:gutjnl-2024-333397 [Epub ahead of print].
The link between gut microbiome and eating behaviours, especially palatable food intake, is a growing focus of scientific investigation. The complex ecosystem of microorganisms in the gut influences host metabolism, immune function and neurobehavioural signalling. This review explores the role of neuroinflammation in dysregulations of food-induced reward signalling and the potential causal role of the gut microbiota on these proinflammatory processes. Particular attention is given to eating disorders (ED, specifically anorexia nervosa, binge eating disorder and bulimia nervosa) and potential links with the gut microbiota, food reward alterations and neuroinflammation. Finally, we propose gut microbiota modulation as a promising therapeutic strategy in food reward alterations and ED.
Additional Links: PMID-39961644
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PubMed:
Citation:
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@article {pmid39961644,
year = {2025},
author = {Huwart, SJP and Morales-Puerto, N and Everard, A},
title = {Gut microbiota-related neuroinflammation at the crossroad of food reward alterations: implications for eating disorders.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333397},
pmid = {39961644},
issn = {1468-3288},
abstract = {The link between gut microbiome and eating behaviours, especially palatable food intake, is a growing focus of scientific investigation. The complex ecosystem of microorganisms in the gut influences host metabolism, immune function and neurobehavioural signalling. This review explores the role of neuroinflammation in dysregulations of food-induced reward signalling and the potential causal role of the gut microbiota on these proinflammatory processes. Particular attention is given to eating disorders (ED, specifically anorexia nervosa, binge eating disorder and bulimia nervosa) and potential links with the gut microbiota, food reward alterations and neuroinflammation. Finally, we propose gut microbiota modulation as a promising therapeutic strategy in food reward alterations and ED.},
}
RevDate: 2025-02-17
Systematical Comparison Reveals Distinct Brain Transcriptomic Characteristics in Depression Models Induced by Gut Microbiota Dysbiosis and Chronic Stress.
Molecular neurobiology [Epub ahead of print].
Major depressive disorder (MDD) is a devastating psychiatric illness with various etiologies. Both chronic stress and gut microbiome dysbiosis are implicated in the pathogenesis of MDD. However, limited research has been conducted to delineate the distinct effects of these two pathogenic factors on the brain transcriptome. We generated and compared transcriptomic features of the anterior cingulate cortex (ACC) from depressive-like mice induced by gut microbiome dysbiosis and canonical chronic stress paradigms, focusing on gene expression patterns and network characteristics. Data derived from MDD patients served as a reference standard to filter the molecular alterations associated with the disorder. Chronic stress induced a plethora of altered genes and biological functions associated with depression, prominently involving mitochondrial dysfunction. However, gut microbiota dysbiosis specifically regulated narrower range of genes and biological mechanisms, targeting aberrations in vesicular transport systems and perturbations of autophagy pathways. Network analysis revealed that hierarchical gene co-expression was specifically affected by gut microbiota dysbiosis rather than chronic stress. Further functional clustering analysis, along with the central distribution of inflammation-related differentially expressed genes, suggested an intricate interplay between disrupted autophagy processes, microglia-mediated inflammation, and synaptic dysfunctions in the network influenced by gut microbiota dysbiosis. Our findings reveal the distinctive transcriptomic alterations of brain shaped by gut microbiota and chronic stress in the development of MDD, contributing to a deeper understanding the heterogeneity of depression. Additionally, we provide a valuable data resource and bioinformatic analysis template for future studies.
Additional Links: PMID-39960648
PubMed:
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@article {pmid39960648,
year = {2025},
author = {Gui, S and Liu, Y and Pu, J and Wang, D and Zhong, X and Chen, W and Chen, X and Chen, Y and Chen, X and Tao, W and Xie, P},
title = {Systematical Comparison Reveals Distinct Brain Transcriptomic Characteristics in Depression Models Induced by Gut Microbiota Dysbiosis and Chronic Stress.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {39960648},
issn = {1559-1182},
support = {2022MD723735//The China Postdoctoral Science Foundation/ ; CSTB2022NSCQ-BHX0011//The Chongqing Natural Science Foundation/ ; cstc2022ycjh-bgzxm0033//The Natural Science Foundation of Chongqing/ ; 82101596//The Natural Science Foundation Project of China/ ; 2021QNRC001//The Young Elite Scientists Sponsorship Program by CAST/ ; 2023CCXM003//The Joint project of Chongqing Municipal Science and Technology Bureau and Chongqing Health Commission/ ; },
abstract = {Major depressive disorder (MDD) is a devastating psychiatric illness with various etiologies. Both chronic stress and gut microbiome dysbiosis are implicated in the pathogenesis of MDD. However, limited research has been conducted to delineate the distinct effects of these two pathogenic factors on the brain transcriptome. We generated and compared transcriptomic features of the anterior cingulate cortex (ACC) from depressive-like mice induced by gut microbiome dysbiosis and canonical chronic stress paradigms, focusing on gene expression patterns and network characteristics. Data derived from MDD patients served as a reference standard to filter the molecular alterations associated with the disorder. Chronic stress induced a plethora of altered genes and biological functions associated with depression, prominently involving mitochondrial dysfunction. However, gut microbiota dysbiosis specifically regulated narrower range of genes and biological mechanisms, targeting aberrations in vesicular transport systems and perturbations of autophagy pathways. Network analysis revealed that hierarchical gene co-expression was specifically affected by gut microbiota dysbiosis rather than chronic stress. Further functional clustering analysis, along with the central distribution of inflammation-related differentially expressed genes, suggested an intricate interplay between disrupted autophagy processes, microglia-mediated inflammation, and synaptic dysfunctions in the network influenced by gut microbiota dysbiosis. Our findings reveal the distinctive transcriptomic alterations of brain shaped by gut microbiota and chronic stress in the development of MDD, contributing to a deeper understanding the heterogeneity of depression. Additionally, we provide a valuable data resource and bioinformatic analysis template for future studies.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Translating Extracellular Electron Transfer Activities with Organic Electrochemical Transistors.
Journal of visualized experiments : JoVE.
Extracellular electron transfer (EET) is a process through which certain microorganisms can transfer electrons across their cell membranes to external electron acceptors, linking cellular metabolism to their environment. While Geobacter and Shewanella have been the primary models for EET research, emerging studies reveal that EET-active species are also associated with fermentation and the human gut microbiome. Leveraging the ability of EET to bridge biological and electronic systems, we present a protocol for using organic electrochemical transistors (OECTs) to translate microbial EET activity into easily detectable electrical signals. This system enables the use of cellular responses to external stimuli for biosensing and biocomputing applications. Specifically, we demonstrated the de-doping of the p-type poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT: PSS) channel in the OECT is driven by cellular EET from Shewanella oneidensis. By transcriptionally controlling EET flux by genetic circuits, we establish the biosensing capability of this hybrid OECT system to detect chemical stimuli, such as inducer molecules. Furthermore, we introduce plasmid-based Boolean logic gates within the cells, allowing them to process environmental signals and drive current changes in the OECTs, further demonstrating the biocomputing potential of these devices. This method provides a novel interface between biological systems and electronics, enabling future high-throughput screening, biosensing, and biocomputing applications.
Additional Links: PMID-39960190
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PubMed:
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@article {pmid39960190,
year = {2025},
author = {Gao, Y and Zhou, Y and Ji, X and Graham, AJ and Dundas, CM and Miniel Mahfoud, IE and Tibbett, BM and Tan, B and Partipilo, G and Dodabalapur, A and Rivnay, J and Keitz, BK},
title = {Translating Extracellular Electron Transfer Activities with Organic Electrochemical Transistors.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {215},
pages = {},
doi = {10.3791/67928},
pmid = {39960190},
issn = {1940-087X},
mesh = {*Shewanella/metabolism ; Electron Transport ; *Transistors, Electronic ; Polystyrenes/chemistry ; Geobacter/metabolism ; Electrochemical Techniques/methods/instrumentation ; Bridged Bicyclo Compounds, Heterocyclic/chemistry ; Thiophenes ; },
abstract = {Extracellular electron transfer (EET) is a process through which certain microorganisms can transfer electrons across their cell membranes to external electron acceptors, linking cellular metabolism to their environment. While Geobacter and Shewanella have been the primary models for EET research, emerging studies reveal that EET-active species are also associated with fermentation and the human gut microbiome. Leveraging the ability of EET to bridge biological and electronic systems, we present a protocol for using organic electrochemical transistors (OECTs) to translate microbial EET activity into easily detectable electrical signals. This system enables the use of cellular responses to external stimuli for biosensing and biocomputing applications. Specifically, we demonstrated the de-doping of the p-type poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT: PSS) channel in the OECT is driven by cellular EET from Shewanella oneidensis. By transcriptionally controlling EET flux by genetic circuits, we establish the biosensing capability of this hybrid OECT system to detect chemical stimuli, such as inducer molecules. Furthermore, we introduce plasmid-based Boolean logic gates within the cells, allowing them to process environmental signals and drive current changes in the OECTs, further demonstrating the biocomputing potential of these devices. This method provides a novel interface between biological systems and electronics, enabling future high-throughput screening, biosensing, and biocomputing applications.},
}
MeSH Terms:
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*Shewanella/metabolism
Electron Transport
*Transistors, Electronic
Polystyrenes/chemistry
Geobacter/metabolism
Electrochemical Techniques/methods/instrumentation
Bridged Bicyclo Compounds, Heterocyclic/chemistry
Thiophenes
RevDate: 2025-02-17
Profiling and metabolic analysis of microorganisms in bioretention cells vegetated with vetiver and cattail species treating nitrogen and phosphorous.
International journal of phytoremediation [Epub ahead of print].
Bioretention cells (BRCs) are increasingly used to treat nutrients in stormwater runoff, with plants known to enhance nitrogen (TN) and phosphorus (TP) uptake. This study investigated the role of rhizosphere microbial communities in TN, TP, and COD removal across three BRCs: an unvegetated control (CP), one vegetated with vetiver (P1), and another with cattail (P2). Detailed microbiome profiling revealed key taxa across phylum, family, and genus levels contributing to nutrient cycling, with P2 showing the highest species richness and diversity based on OTU counts and diversity indices. Proteobacteria, Acidobacteria, and Verrucomicrobiota were the most prominent phyla, aligning with their known roles in nutrient uptake. Key functional taxa included denitrifiers (e.g., Ramlibacter, TRA3-20), Ammonia Oxidizing Bacteria (AOBs) (e.g., MND1, Ellin 6067), and Phosphate Accumulating Organisms (PAOs) (e.g., Comamonadaceae, Vicinamibacteria), supporting TN (>79%) and TP (>84%) removal rates. Distinct microbial compositions between vegetated BRCs confirmed the role of root exudates in microbial selection and enhanced nutrient removal. These findings emphasize the importance of plant-specific rhizosphere effects and microbial selection in optimizing BRC design for stormwater treatment applications.
Additional Links: PMID-39960092
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PubMed:
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@article {pmid39960092,
year = {2025},
author = {Narayanasamydamodaran, S and Kumar, N and Zuo, J},
title = {Profiling and metabolic analysis of microorganisms in bioretention cells vegetated with vetiver and cattail species treating nitrogen and phosphorous.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/15226514.2025.2452942},
pmid = {39960092},
issn = {1549-7879},
abstract = {Bioretention cells (BRCs) are increasingly used to treat nutrients in stormwater runoff, with plants known to enhance nitrogen (TN) and phosphorus (TP) uptake. This study investigated the role of rhizosphere microbial communities in TN, TP, and COD removal across three BRCs: an unvegetated control (CP), one vegetated with vetiver (P1), and another with cattail (P2). Detailed microbiome profiling revealed key taxa across phylum, family, and genus levels contributing to nutrient cycling, with P2 showing the highest species richness and diversity based on OTU counts and diversity indices. Proteobacteria, Acidobacteria, and Verrucomicrobiota were the most prominent phyla, aligning with their known roles in nutrient uptake. Key functional taxa included denitrifiers (e.g., Ramlibacter, TRA3-20), Ammonia Oxidizing Bacteria (AOBs) (e.g., MND1, Ellin 6067), and Phosphate Accumulating Organisms (PAOs) (e.g., Comamonadaceae, Vicinamibacteria), supporting TN (>79%) and TP (>84%) removal rates. Distinct microbial compositions between vegetated BRCs confirmed the role of root exudates in microbial selection and enhanced nutrient removal. These findings emphasize the importance of plant-specific rhizosphere effects and microbial selection in optimizing BRC design for stormwater treatment applications.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
A structural equation model predicts chronic wound healing time using patient characteristics and wound microbiome composition.
Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society, 33(1):e70004.
Wound aetiology, host characteristics and the wound microbiome contribute to chronic wound development. Yet, there is little accounting for the relative importance of these factors to predict wound healing. Here, a structural equation model was developed to provide such an explanatory and predictive framework. Chronic wounds from 565 patients treated at a clinic practicing biofilm-based wound care were included. Patient information included DNA sequencing-based wound microbiome clinical reports corresponding to the initial clinical visit. Wound microbiome data was integrated into the SEM as a latent variable using a pre-modelling parcel optimization routine presented herein for the first time (available as R library parcelR). A microbiome latent construct associated with improved healing was validated, and the final SEM included this latent construct plus three species associated with diminished healing (Anaerococcus vaginalis, Finegoldia magna and Pseudomonas aeruginosa), as well as smoking, wound volume, slough, exudate, edema, percent granulation and wound etiology. This model explained 46% of variations in healing time, with the microbiome contributing the largest proportion of variance explained. Model validity was confirmed with an independent cohort (n = 79) through which ~60% of the variation in healing time was predicted. This model can serve as a foundation for the development of a predictive tool that may have clinical utility.
Additional Links: PMID-39959986
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@article {pmid39959986,
year = {2025},
author = {Ancira, J and Gabrilska, R and Tipton, C and Miller, C and Stickley, Z and Omeir, K and Wakeman, C and Little, T and Wolcott, J and Philips, CD},
title = {A structural equation model predicts chronic wound healing time using patient characteristics and wound microbiome composition.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {1},
pages = {e70004},
doi = {10.1111/wrr.70004},
pmid = {39959986},
issn = {1524-475X},
support = {R15GM141973/NH/NIH HHS/United States ; },
mesh = {Humans ; *Wound Healing/physiology ; *Microbiota ; Male ; Female ; Chronic Disease ; Middle Aged ; Wounds and Injuries/microbiology ; Aged ; Time Factors ; Biofilms/growth & development ; Adult ; },
abstract = {Wound aetiology, host characteristics and the wound microbiome contribute to chronic wound development. Yet, there is little accounting for the relative importance of these factors to predict wound healing. Here, a structural equation model was developed to provide such an explanatory and predictive framework. Chronic wounds from 565 patients treated at a clinic practicing biofilm-based wound care were included. Patient information included DNA sequencing-based wound microbiome clinical reports corresponding to the initial clinical visit. Wound microbiome data was integrated into the SEM as a latent variable using a pre-modelling parcel optimization routine presented herein for the first time (available as R library parcelR). A microbiome latent construct associated with improved healing was validated, and the final SEM included this latent construct plus three species associated with diminished healing (Anaerococcus vaginalis, Finegoldia magna and Pseudomonas aeruginosa), as well as smoking, wound volume, slough, exudate, edema, percent granulation and wound etiology. This model explained 46% of variations in healing time, with the microbiome contributing the largest proportion of variance explained. Model validity was confirmed with an independent cohort (n = 79) through which ~60% of the variation in healing time was predicted. This model can serve as a foundation for the development of a predictive tool that may have clinical utility.},
}
MeSH Terms:
show MeSH Terms
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Humans
*Wound Healing/physiology
*Microbiota
Male
Female
Chronic Disease
Middle Aged
Wounds and Injuries/microbiology
Aged
Time Factors
Biofilms/growth & development
Adult
RevDate: 2025-02-17
CmpDate: 2025-02-17
The microbiome as a modulator of neurological health across the maternal-offspring interface.
The Journal of clinical investigation, 135(4): pii:184314.
The maternal microbiome is emerging as an important factor that influences the neurological health of mothers and their children. Recent studies highlight how microbial communities in the maternal gut can shape early-life development in ways that inform long-term health trajectories. Research on the neurodevelopmental effects of maternal microbiomes is expanding our understanding of the microbiome-gut-brain axis to include signaling across the maternal-offspring unit during the perinatal period. In this Review, we synthesize existing literature on how the maternal microbiome modulates brain function and behavior in both mothers and their developing offspring. We present evidence from human and animal studies showing that the maternal microbiome interacts with environmental factors to impact risk for neurodevelopmental abnormalities. We further discuss molecular and cellular mechanisms that facilitate maternal-offspring crosstalk for neuromodulation. Finally, we consider how advancing understanding of these complex interactions could lead to microbiome-based interventions for promoting maternal and offspring health.
Additional Links: PMID-39959974
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PubMed:
Citation:
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@article {pmid39959974,
year = {2025},
author = {Orchanian, SB and Hsiao, EY},
title = {The microbiome as a modulator of neurological health across the maternal-offspring interface.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {4},
pages = {},
doi = {10.1172/JCI184314},
pmid = {39959974},
issn = {1558-8238},
mesh = {Humans ; Female ; Animals ; *Gastrointestinal Microbiome ; Pregnancy ; Brain-Gut Axis/physiology ; Neurodevelopmental Disorders/microbiology ; Brain/microbiology ; },
abstract = {The maternal microbiome is emerging as an important factor that influences the neurological health of mothers and their children. Recent studies highlight how microbial communities in the maternal gut can shape early-life development in ways that inform long-term health trajectories. Research on the neurodevelopmental effects of maternal microbiomes is expanding our understanding of the microbiome-gut-brain axis to include signaling across the maternal-offspring unit during the perinatal period. In this Review, we synthesize existing literature on how the maternal microbiome modulates brain function and behavior in both mothers and their developing offspring. We present evidence from human and animal studies showing that the maternal microbiome interacts with environmental factors to impact risk for neurodevelopmental abnormalities. We further discuss molecular and cellular mechanisms that facilitate maternal-offspring crosstalk for neuromodulation. Finally, we consider how advancing understanding of these complex interactions could lead to microbiome-based interventions for promoting maternal and offspring health.},
}
MeSH Terms:
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hide MeSH Terms
Humans
Female
Animals
*Gastrointestinal Microbiome
Pregnancy
Brain-Gut Axis/physiology
Neurodevelopmental Disorders/microbiology
Brain/microbiology
RevDate: 2025-02-17
CmpDate: 2025-02-17
Microbial influencers: the airway microbiome's role in asthma.
The Journal of clinical investigation, 135(4): pii:184316.
Asthma is a common chronic respiratory disease affecting people of all ages globally. The airway hosts diverse microbial communities increasingly recognized as influential in the development and disease course of asthma. Here, we review recent findings on the airway microbiome in asthma. As relationships between the airway microbiome and respiratory health take root early in life, we first provide an overview of the early-life airway microbiome and asthma development, where multiple cohort studies have identified bacterial genera in the infant airway associated with risk of future wheeze and asthma. We then address current understandings of interactions between environmental factors, the airway microbiome, and asthma, including the effects of rural/urban environments, pet ownership, smoking, viral illness, and antibiotics. Next, we delve into what has been observed about the airway microbiome and asthma phenotypes and endotypes, as airway microbiota have been associated with asthma control, severity, obesity-related asthma, and treatment effects as well as with type 2 high, type 2 low, and more newly described multi-omic asthma endotypes. We then discuss emerging approaches to shape the microbiome for asthma therapy and conclude the Review with perspectives on future research directions.
Additional Links: PMID-39959969
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PubMed:
Citation:
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@article {pmid39959969,
year = {2025},
author = {Kim, YJ and Bunyavanich, S},
title = {Microbial influencers: the airway microbiome's role in asthma.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {4},
pages = {},
doi = {10.1172/JCI184316},
pmid = {39959969},
issn = {1558-8238},
mesh = {*Asthma/microbiology/immunology ; Humans ; *Microbiota/immunology ; Animals ; Respiratory System/microbiology/immunology ; },
abstract = {Asthma is a common chronic respiratory disease affecting people of all ages globally. The airway hosts diverse microbial communities increasingly recognized as influential in the development and disease course of asthma. Here, we review recent findings on the airway microbiome in asthma. As relationships between the airway microbiome and respiratory health take root early in life, we first provide an overview of the early-life airway microbiome and asthma development, where multiple cohort studies have identified bacterial genera in the infant airway associated with risk of future wheeze and asthma. We then address current understandings of interactions between environmental factors, the airway microbiome, and asthma, including the effects of rural/urban environments, pet ownership, smoking, viral illness, and antibiotics. Next, we delve into what has been observed about the airway microbiome and asthma phenotypes and endotypes, as airway microbiota have been associated with asthma control, severity, obesity-related asthma, and treatment effects as well as with type 2 high, type 2 low, and more newly described multi-omic asthma endotypes. We then discuss emerging approaches to shape the microbiome for asthma therapy and conclude the Review with perspectives on future research directions.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Asthma/microbiology/immunology
Humans
*Microbiota/immunology
Animals
Respiratory System/microbiology/immunology
RevDate: 2025-02-17
Bile acid and microbiome interactions in the developing child.
Journal of pediatric gastroenterology and nutrition [Epub ahead of print].
Interactions between the gut microbiome and bile acids are complex and are linked to outcomes in pediatric liver disease by mechanisms that are incompletely understood. In adults, primary bile acids are synthesized in the liver and secreted into the intestine, where complex communities of gut microbes deconjugate, oxidize, epimerize, and 7α-dehydroxylate bile acids into a diverse array of unconjugated, secondary, allo-, iso-, and oxo-bile acids. In contrast, the infant gut microbiota contains a simple, Bifidobacterium-dominant community that transitions to a more diverse, adult-like community as additional microbes colonize the gut. This microbial succession gradually confers deconjugation, oxidation, epimerization, and 7α-dehydroxylation activities that mature the bile acid pool from a profile dominated by primary bile acids early in life to a more diverse, adult-like bile acid profile in later childhood. Altered bile acid profiles in pediatric cholestatic disorders have the potential to change the developmental trajectory of the microbiome. Conversely, alterations in the gut microbiome may re-shape the bile acid pool and hepatic bile acid metabolism. Understanding the mechanisms underlying these interactions will increase our understanding of liver pathophysiology and will motivate new therapeutic strategies for pediatric hepatic disorders. This review aims to highlight differences between the pediatric and adult intestinal microbiome and bile acid pool, and to discuss interactions between gut microbes and bile acids that are critical in early life and that may impact outcomes in infants and children with cholestatic liver disease, including biliary atresia.
Additional Links: PMID-39959949
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PubMed:
Citation:
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@article {pmid39959949,
year = {2025},
author = {Tessier, MEM and Shneider, BL and Petrosino, JF and Preidis, GA},
title = {Bile acid and microbiome interactions in the developing child.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70014},
pmid = {39959949},
issn = {1536-4801},
support = {5K23DK119567//NIH NIDDK/ ; },
abstract = {Interactions between the gut microbiome and bile acids are complex and are linked to outcomes in pediatric liver disease by mechanisms that are incompletely understood. In adults, primary bile acids are synthesized in the liver and secreted into the intestine, where complex communities of gut microbes deconjugate, oxidize, epimerize, and 7α-dehydroxylate bile acids into a diverse array of unconjugated, secondary, allo-, iso-, and oxo-bile acids. In contrast, the infant gut microbiota contains a simple, Bifidobacterium-dominant community that transitions to a more diverse, adult-like community as additional microbes colonize the gut. This microbial succession gradually confers deconjugation, oxidation, epimerization, and 7α-dehydroxylation activities that mature the bile acid pool from a profile dominated by primary bile acids early in life to a more diverse, adult-like bile acid profile in later childhood. Altered bile acid profiles in pediatric cholestatic disorders have the potential to change the developmental trajectory of the microbiome. Conversely, alterations in the gut microbiome may re-shape the bile acid pool and hepatic bile acid metabolism. Understanding the mechanisms underlying these interactions will increase our understanding of liver pathophysiology and will motivate new therapeutic strategies for pediatric hepatic disorders. This review aims to highlight differences between the pediatric and adult intestinal microbiome and bile acid pool, and to discuss interactions between gut microbes and bile acids that are critical in early life and that may impact outcomes in infants and children with cholestatic liver disease, including biliary atresia.},
}
RevDate: 2025-02-17
Deciphering the microbiome dynamics in an effective banana Fusarium wilt biocontrol interaction system.
3 Biotech, 15(3):59.
UNLABELLED: This study explored the effects of bacterial and fungal biocontrol agents (consortia) on the microbiome of Fusarium wilt (Foc TR4)-infected Cavandish banana soils in terms of alteration of prevalence and abundance. The results showed a significant shift in microbial diversity, dominance, abundance, evenness, richness and composition core and indicator microbiome in response to soil applied consortia and untreated controls. A total of 2857 bacterial OTUs from 331 families across 40 phyla dominated with Bacillaceae (40.2%), Acidobacteriaceae (14.2%), Haloarculaceae (12.6%), and Paenibacillaceae (9.4%). There were 4,868 fungal OTUs from 520 families across 18 phyla dominant with Mortierellaceae (20.9%), Cortinariaceae (7.6%), Aspergillaceae (6.2%), Pandeidae (5.6%), and Pyronemataceae (5.0%). Alpha diversity analysis indicated that bacterial diversity varied across treatments where T2 has the highest OTUs, while fungal diversity remained relatively stable across the treatments. Beta diversity and PCoA analysis revealed the differences in community compositions across treatments in both bacterial and fungal microbiome. Bacterial communities in T3 and T5 were highly similar, whereas T4 had a notable difference in fungal communities. This study identified a total of 192 bacterial core OTUs dominated with Firmicutes, Proteobacteria, and Acidobacteriia. In the case of fungi, 59 core OTUs from Ascomycota, Basidiomycota, and Mucoromycota are the most abundant ones within the treatments. Venn diagram revealed unique, common and shared OTUs suggesting antagonistic interactions of the soil applied consortia. DESeq2 analysis revealed a significant shift of core microbiome, where positive fold changes in Betaproteobacteria for bacterial, and Fusarium sp. for fungi were noticeable. Heatmap analysis revealed the treatment-dependent differences in community composition where T2 has higher bacterial abundance and T4 has higher fungal abundance suggesting that the biocontrol treatments affect the soil microbiome differently depending on the combinations and the origins of the consortia. The indicator species analysis identified 37 bacterial and 34 fungal OTUs that were specific and indicative of particular treatments that suggest microbial consortia might be selectively enhancing the growth of functionally beneficial microbial populations of the soil that promote soil health and disease suppressiveness. This study recommends that the use of biocontrol agents in the form of consortia would not only expand the diversity of the soil microbiome but also improve the effectiveness and the sustainability of Fusarium wilt management.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04223-7.
Additional Links: PMID-39959709
PubMed:
Citation:
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@article {pmid39959709,
year = {2025},
author = {Hadimani, A and Raman, T and Esack, E and Loganathan, M and Jaganathan, D and Kantharaju, V and Selvarajan, R},
title = {Deciphering the microbiome dynamics in an effective banana Fusarium wilt biocontrol interaction system.},
journal = {3 Biotech},
volume = {15},
number = {3},
pages = {59},
pmid = {39959709},
issn = {2190-572X},
abstract = {UNLABELLED: This study explored the effects of bacterial and fungal biocontrol agents (consortia) on the microbiome of Fusarium wilt (Foc TR4)-infected Cavandish banana soils in terms of alteration of prevalence and abundance. The results showed a significant shift in microbial diversity, dominance, abundance, evenness, richness and composition core and indicator microbiome in response to soil applied consortia and untreated controls. A total of 2857 bacterial OTUs from 331 families across 40 phyla dominated with Bacillaceae (40.2%), Acidobacteriaceae (14.2%), Haloarculaceae (12.6%), and Paenibacillaceae (9.4%). There were 4,868 fungal OTUs from 520 families across 18 phyla dominant with Mortierellaceae (20.9%), Cortinariaceae (7.6%), Aspergillaceae (6.2%), Pandeidae (5.6%), and Pyronemataceae (5.0%). Alpha diversity analysis indicated that bacterial diversity varied across treatments where T2 has the highest OTUs, while fungal diversity remained relatively stable across the treatments. Beta diversity and PCoA analysis revealed the differences in community compositions across treatments in both bacterial and fungal microbiome. Bacterial communities in T3 and T5 were highly similar, whereas T4 had a notable difference in fungal communities. This study identified a total of 192 bacterial core OTUs dominated with Firmicutes, Proteobacteria, and Acidobacteriia. In the case of fungi, 59 core OTUs from Ascomycota, Basidiomycota, and Mucoromycota are the most abundant ones within the treatments. Venn diagram revealed unique, common and shared OTUs suggesting antagonistic interactions of the soil applied consortia. DESeq2 analysis revealed a significant shift of core microbiome, where positive fold changes in Betaproteobacteria for bacterial, and Fusarium sp. for fungi were noticeable. Heatmap analysis revealed the treatment-dependent differences in community composition where T2 has higher bacterial abundance and T4 has higher fungal abundance suggesting that the biocontrol treatments affect the soil microbiome differently depending on the combinations and the origins of the consortia. The indicator species analysis identified 37 bacterial and 34 fungal OTUs that were specific and indicative of particular treatments that suggest microbial consortia might be selectively enhancing the growth of functionally beneficial microbial populations of the soil that promote soil health and disease suppressiveness. This study recommends that the use of biocontrol agents in the form of consortia would not only expand the diversity of the soil microbiome but also improve the effectiveness and the sustainability of Fusarium wilt management.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04223-7.},
}
RevDate: 2025-02-17
Lactic acid bacteria in Swedish honey bees during outbreaks of American foulbrood.
Ecology and evolution, 14(2):e10964.
The honey bee microbiota is involved in several important functions, and alterations in the composition could have a severe effect on honey bee health. Among the bacteria identified in the honey bee microbiome are a group of non-pathogenic honey bee-specific lactic acid bacteria (hbs-LAB) that have been shown to inhibit the growth of bacterial pathogens such as Paenibacillus larvae, the causative agent of American foulbrood (AFB). While P. larvae only causes disease in larvae and not in adult honey bees, there are reports of the pathogen causing changes in the microbiota composition of the adults. The aim of this study was to investigate how AFB in the colony affect the hbs-LAB composition in adult honey bees. Adult bees were collected from colonies with and without AFB during three outbreaks of AFB in Sweden. The hbs-LAB was analyzed using qPCR to detect and quantify the number of ten hbs-LAB (five Lactobacilli, two Apilactobacilli, one Bombilactobacilli, and two Bifidobacterium). The hbs-LAB composition was compared between AFB outbreaks and depending on the AFB status of the honeybee colony at the time of sampling. The data analyses revealed differences in the abundance of individual hbs-LAB between outbreaks and an overall difference in bacterial community composition depending on AFB status. Also, a higher hbs-LAB diversity was observed in samples that were P. larvae culture positive.
Additional Links: PMID-39959658
PubMed:
Citation:
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@article {pmid39959658,
year = {2024},
author = {Nilsson, A and D'Alvise, P and Milbrath, MO and Forsgren, E},
title = {Lactic acid bacteria in Swedish honey bees during outbreaks of American foulbrood.},
journal = {Ecology and evolution},
volume = {14},
number = {2},
pages = {e10964},
pmid = {39959658},
issn = {2045-7758},
abstract = {The honey bee microbiota is involved in several important functions, and alterations in the composition could have a severe effect on honey bee health. Among the bacteria identified in the honey bee microbiome are a group of non-pathogenic honey bee-specific lactic acid bacteria (hbs-LAB) that have been shown to inhibit the growth of bacterial pathogens such as Paenibacillus larvae, the causative agent of American foulbrood (AFB). While P. larvae only causes disease in larvae and not in adult honey bees, there are reports of the pathogen causing changes in the microbiota composition of the adults. The aim of this study was to investigate how AFB in the colony affect the hbs-LAB composition in adult honey bees. Adult bees were collected from colonies with and without AFB during three outbreaks of AFB in Sweden. The hbs-LAB was analyzed using qPCR to detect and quantify the number of ten hbs-LAB (five Lactobacilli, two Apilactobacilli, one Bombilactobacilli, and two Bifidobacterium). The hbs-LAB composition was compared between AFB outbreaks and depending on the AFB status of the honeybee colony at the time of sampling. The data analyses revealed differences in the abundance of individual hbs-LAB between outbreaks and an overall difference in bacterial community composition depending on AFB status. Also, a higher hbs-LAB diversity was observed in samples that were P. larvae culture positive.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Acupuncture mediates the "gut-testis axis" to improve asthenozoospermia.
Frontiers in endocrinology, 16:1514010.
BACKGROUND: Asthenozoospermia is a common cause of male infertility. Studies have shown that sperm quality and motility are affected by the gut-testis axis that can regulate testicular metabolism and function through the gut microbiota and its metabolites. Acupuncture is an important modality of complementary and alternative medicine. It can improve sperm motility, but it remains unclear whether acupuncture can enhance sperm vitality by influencing the gut-testis axis.
METHODS: In this study, sperm quality, testicular pathology, and serum hormone levels were assessed using a cyclophosphamide-induced mouse model. Real-time PCR, a western blot analysis, and immunofluorescence techniques were used to assess the effects of acupuncture on the gut barrier and blood-testis barrier functions. In addition, gut microbiome and metabolomics were used to study the impact of acupuncture on the gut microbiota structure, serum, and testicular metabolites in asthenozoospermic mice. Further validation was obtained by performing a fecal microbiota transplantation (FMT).
RESULTS: Acupuncture improved the sperm quality; ameliorated testicular pathology; increased serum testosterone (T), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) levels; and repaired gut and blood-testis barrier damage in asthenozoospermic mice. The abundances of Bacteroidota, Firmicutes, Faecalibaculum, and Dubosiella were associated with sperm motility, as shown by a gut microbiome analysis. Serum metabolomics revealed that differentially expressed metabolites (DEMs), such as cytosine and N-oleyl-leucine, were closely related to sperm motility. Testicular metabolomics analysis revealed DEMs, such as 5-fluorouridine and 1-acetylimidazole, were also associated with sperm motility. Furthermore, reproductive function improvements in asthenozoospermic mice through acupuncture were achieved via an FMT.
CONCLUSION: Acupuncture may alleviate asthenozoospermia symptoms by modulating the gut-testis axis and repairing the gut-testis barrier.
Additional Links: PMID-39959619
PubMed:
Citation:
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@article {pmid39959619,
year = {2025},
author = {Hao, J and Xu, H and Chang, B and Ren, J and Wang, H and Ji, L},
title = {Acupuncture mediates the "gut-testis axis" to improve asthenozoospermia.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1514010},
pmid = {39959619},
issn = {1664-2392},
mesh = {Male ; Animals ; *Asthenozoospermia/therapy/metabolism ; Mice ; *Testis/metabolism ; *Acupuncture Therapy ; *Sperm Motility ; Gastrointestinal Microbiome/physiology ; Spermatozoa/metabolism ; Disease Models, Animal ; Blood-Testis Barrier/metabolism ; },
abstract = {BACKGROUND: Asthenozoospermia is a common cause of male infertility. Studies have shown that sperm quality and motility are affected by the gut-testis axis that can regulate testicular metabolism and function through the gut microbiota and its metabolites. Acupuncture is an important modality of complementary and alternative medicine. It can improve sperm motility, but it remains unclear whether acupuncture can enhance sperm vitality by influencing the gut-testis axis.
METHODS: In this study, sperm quality, testicular pathology, and serum hormone levels were assessed using a cyclophosphamide-induced mouse model. Real-time PCR, a western blot analysis, and immunofluorescence techniques were used to assess the effects of acupuncture on the gut barrier and blood-testis barrier functions. In addition, gut microbiome and metabolomics were used to study the impact of acupuncture on the gut microbiota structure, serum, and testicular metabolites in asthenozoospermic mice. Further validation was obtained by performing a fecal microbiota transplantation (FMT).
RESULTS: Acupuncture improved the sperm quality; ameliorated testicular pathology; increased serum testosterone (T), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) levels; and repaired gut and blood-testis barrier damage in asthenozoospermic mice. The abundances of Bacteroidota, Firmicutes, Faecalibaculum, and Dubosiella were associated with sperm motility, as shown by a gut microbiome analysis. Serum metabolomics revealed that differentially expressed metabolites (DEMs), such as cytosine and N-oleyl-leucine, were closely related to sperm motility. Testicular metabolomics analysis revealed DEMs, such as 5-fluorouridine and 1-acetylimidazole, were also associated with sperm motility. Furthermore, reproductive function improvements in asthenozoospermic mice through acupuncture were achieved via an FMT.
CONCLUSION: Acupuncture may alleviate asthenozoospermia symptoms by modulating the gut-testis axis and repairing the gut-testis barrier.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Male
Animals
*Asthenozoospermia/therapy/metabolism
Mice
*Testis/metabolism
*Acupuncture Therapy
*Sperm Motility
Gastrointestinal Microbiome/physiology
Spermatozoa/metabolism
Disease Models, Animal
Blood-Testis Barrier/metabolism
RevDate: 2025-02-17
Artificial intelligence use for precision medicine in inflammatory bowel disease: a systematic review.
American journal of translational research, 17(1):28-46.
INTRODUCTION: Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, presents significant clinical challenges due to its heterogeneous nature and complex etiology. Recent advancements in biomedical research have enhanced our understanding of IBD's genetic, microbial, and biochemical aspects. However, persistent issues in clinical management, including treatment non-response, surgical interventions, and diagnostic uncertainties, underscore the need for more targeted approaches. This review examines the convergence of artificial intelligence (AI) and precision medicine (PM) in IBD management. By leveraging AI's capacity to analyze complex, multi-dimensional datasets, this emerging field offers promising applications in improving diagnostic accuracy, predicting treatment responses, and forecasting disease progression, potentially transforming IBD patient care.
METHOD: The systematic review (SR) was conducted by searching the following databases: PubMed, PubMed PMC, BVS, Scopus, Web of Science, Embase, Cochrane, and ProQuest up to February 2024. Studies that employed AI in IBD applied to precision medicine were included.
RESULTS: 139 studies on applying AI in precision medicine for IBD were identified. Most studies (>70%) were published after 2020, indicating a recent surge in interest. The AI applications primarily focused on diagnosis, treatment response prediction, and prognosis. Machine learning algorithms were predominantly used, particularly random forest, logistic regression, and support vector machines. Omics data were frequently employed as predictors, especially transcriptomics and microbiome analyses. Studies demonstrated good predictive performance across all three areas, with median AUC values ranging from 0.85 to 0.90.
CONCLUSION: AI applications in IBD show promising potential to enhance clinical practice, particularly in disease prognosis and predicting treatment response. However, clinical implementation requires further validation through prospective studies. Future research should focus on standardizing protocols, defining clinically significant outcomes, and evaluating the efficacy of these tools.
Additional Links: PMID-39959235
PubMed:
Citation:
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@article {pmid39959235,
year = {2025},
author = {Ceccato, HD and Silva, TAOE and Genaro, LM and Silva, JF and de Souza, WM and Oliveira, PSP and de Azevedo, AT and Ayrizono, MLS and Leal, RF},
title = {Artificial intelligence use for precision medicine in inflammatory bowel disease: a systematic review.},
journal = {American journal of translational research},
volume = {17},
number = {1},
pages = {28-46},
pmid = {39959235},
issn = {1943-8141},
abstract = {INTRODUCTION: Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, presents significant clinical challenges due to its heterogeneous nature and complex etiology. Recent advancements in biomedical research have enhanced our understanding of IBD's genetic, microbial, and biochemical aspects. However, persistent issues in clinical management, including treatment non-response, surgical interventions, and diagnostic uncertainties, underscore the need for more targeted approaches. This review examines the convergence of artificial intelligence (AI) and precision medicine (PM) in IBD management. By leveraging AI's capacity to analyze complex, multi-dimensional datasets, this emerging field offers promising applications in improving diagnostic accuracy, predicting treatment responses, and forecasting disease progression, potentially transforming IBD patient care.
METHOD: The systematic review (SR) was conducted by searching the following databases: PubMed, PubMed PMC, BVS, Scopus, Web of Science, Embase, Cochrane, and ProQuest up to February 2024. Studies that employed AI in IBD applied to precision medicine were included.
RESULTS: 139 studies on applying AI in precision medicine for IBD were identified. Most studies (>70%) were published after 2020, indicating a recent surge in interest. The AI applications primarily focused on diagnosis, treatment response prediction, and prognosis. Machine learning algorithms were predominantly used, particularly random forest, logistic regression, and support vector machines. Omics data were frequently employed as predictors, especially transcriptomics and microbiome analyses. Studies demonstrated good predictive performance across all three areas, with median AUC values ranging from 0.85 to 0.90.
CONCLUSION: AI applications in IBD show promising potential to enhance clinical practice, particularly in disease prognosis and predicting treatment response. However, clinical implementation requires further validation through prospective studies. Future research should focus on standardizing protocols, defining clinically significant outcomes, and evaluating the efficacy of these tools.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.
Frontiers in cellular and infection microbiology, 15:1511625.
INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.
METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.
RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.
DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.
Additional Links: PMID-39958933
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Citation:
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@article {pmid39958933,
year = {2025},
author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P},
title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1511625},
pmid = {39958933},
issn = {2235-2988},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; },
abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.
METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.
RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.
DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Female
*Endometrial Neoplasms/microbiology/genetics
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Uterus/microbiology
Middle Aged
Phylogeny
Biomarkers
Adult
Aged
Reactive Oxygen Species/metabolism
Carcinogenesis
Fibroblasts/microbiology
Biomarkers, Tumor/genetics
Computational Biology/methods
Oxidative Stress
RevDate: 2025-02-17
Harnessing multi-omics approaches to elucidate the role of Chinese herbal compounds in chemotherapy-induced gastrointestinal damage.
World journal of gastrointestinal oncology, 17(2):101500.
In this editorial, we discuss the findings reported by Wang et al in the latest issue of the World Journal of Gastrointestinal Oncology. Various research methodologies, including microbiome analysis, assert that the Tzu-Chi Cancer-Antagonizing and Life-Protecting II Decoction of Chinese herbal compounds mitigates inflammatory responses by inhibiting the NF-κB signaling pathway. This action helps maintain the dynamic equilibrium of the intestinal microecology and lessens chemotherapy-induced gastrointestinal damage. The efficacy of these compounds is intimately linked to the composition of intestinal microbes. These compounds regulate intestinal microecology by virtue of their specific compatibility and effectiveness, thereby enhancing the overall therapeutic outcomes of cancer chemotherapy. Nonetheless, the exact mechanisms underlying these effects warrant further investigation. Multi-omics technologies offer a systematic approach to elucidate the mechanisms and effectiveness of Chinese herbal compounds in vivo. This manuscript reviews the application of multi-omics technologies to Chinese herbal compounds and explores their potential role in modulating the gastrointestinal microenvironment following cancer chemotherapy, thus providing a theoretical foundation for their continued use in adjunct cancer treatment.
Additional Links: PMID-39958539
PubMed:
Citation:
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@article {pmid39958539,
year = {2025},
author = {Qiao, C and Zhang, HX and Tian, XT and Zhang, YJ and Li, DH},
title = {Harnessing multi-omics approaches to elucidate the role of Chinese herbal compounds in chemotherapy-induced gastrointestinal damage.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {2},
pages = {101500},
pmid = {39958539},
issn = {1948-5204},
abstract = {In this editorial, we discuss the findings reported by Wang et al in the latest issue of the World Journal of Gastrointestinal Oncology. Various research methodologies, including microbiome analysis, assert that the Tzu-Chi Cancer-Antagonizing and Life-Protecting II Decoction of Chinese herbal compounds mitigates inflammatory responses by inhibiting the NF-κB signaling pathway. This action helps maintain the dynamic equilibrium of the intestinal microecology and lessens chemotherapy-induced gastrointestinal damage. The efficacy of these compounds is intimately linked to the composition of intestinal microbes. These compounds regulate intestinal microecology by virtue of their specific compatibility and effectiveness, thereby enhancing the overall therapeutic outcomes of cancer chemotherapy. Nonetheless, the exact mechanisms underlying these effects warrant further investigation. Multi-omics technologies offer a systematic approach to elucidate the mechanisms and effectiveness of Chinese herbal compounds in vivo. This manuscript reviews the application of multi-omics technologies to Chinese herbal compounds and explores their potential role in modulating the gastrointestinal microenvironment following cancer chemotherapy, thus providing a theoretical foundation for their continued use in adjunct cancer treatment.},
}
RevDate: 2025-02-17
Synbiotics and Gut-Heart Axis in Cardiometabolic Disease.
JACC. Basic to translational science, 10(1):16-19.
Additional Links: PMID-39958467
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Citation:
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@article {pmid39958467,
year = {2025},
author = {Sachse, M and Stellos, K},
title = {Synbiotics and Gut-Heart Axis in Cardiometabolic Disease.},
journal = {JACC. Basic to translational science},
volume = {10},
number = {1},
pages = {16-19},
pmid = {39958467},
issn = {2452-302X},
}
RevDate: 2025-02-17
Targeting gut microbiota to regulate the adaptive immune response in atherosclerosis.
Frontiers in cardiovascular medicine, 12:1502124.
Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques in the intima of large and medium-sized arteries. Accumulating evidence indicates the important regulatory role of the adaptive immune system in atherosclerosis during all stages of the disease. The gut microbiome has also become a key regulator of atherosclerosis and immunomodulation. Whilst existing research extensively explores the impact of the microbiome on the innate immune system, only a handful of studies have explored the regulatory capacity of the microbiome on the adaptive immune system to modulate atherogenesis. Building on these concepts and the pitfalls on the gut microbiota and adaptive immune response interaction, this review explores potential strategies to therapeutically target the microbiome, including the use of prebiotics and vaccinations, which could influence the adaptive immune response and consequently plaque composition and development.
Additional Links: PMID-39957996
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Citation:
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@article {pmid39957996,
year = {2025},
author = {Giakomidi, D and Ishola, A and Nus, M},
title = {Targeting gut microbiota to regulate the adaptive immune response in atherosclerosis.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1502124},
pmid = {39957996},
issn = {2297-055X},
abstract = {Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques in the intima of large and medium-sized arteries. Accumulating evidence indicates the important regulatory role of the adaptive immune system in atherosclerosis during all stages of the disease. The gut microbiome has also become a key regulator of atherosclerosis and immunomodulation. Whilst existing research extensively explores the impact of the microbiome on the innate immune system, only a handful of studies have explored the regulatory capacity of the microbiome on the adaptive immune system to modulate atherogenesis. Building on these concepts and the pitfalls on the gut microbiota and adaptive immune response interaction, this review explores potential strategies to therapeutically target the microbiome, including the use of prebiotics and vaccinations, which could influence the adaptive immune response and consequently plaque composition and development.},
}
RevDate: 2025-02-17
Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.
Current research in microbial sciences, 7:100286.
A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.
Additional Links: PMID-39957783
PubMed:
Citation:
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@article {pmid39957783,
year = {2024},
author = {Chattaraj, S and Mitra, D and Chattaraj, M and Ganguly, A and Thatoi, H and Mohapatra, PKD},
title = {Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100286},
pmid = {39957783},
issn = {2666-5174},
abstract = {A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.},
}
RevDate: 2025-02-17
Unraveling the future: hot topics shaping molecular diagnostics Today.
Expert review of molecular diagnostics [Epub ahead of print].
INTRODUCTION: This special report highlights the transformative potential of advanced diagnostic technologies in modern healthcare, emphasizing their role in enhancing disease detection, treatment personalization, and patient outcomes.
AREAS COVERED: Innovations such as Next-Generation Sequencing (NGS), liquid biopsy, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -based diagnostics, Point-of-Care (PoC) testing, microbiome analysis, and Artificial Intelligence are reshaping the diagnostic landscape. These methods facilitate early identification of diseases, enable tailored therapies based on individual genetic profiles, and provide noninvasive monitoring options. Furthermore, telemedicine enhances access to care while reducing costs associated with traditional healthcare delivery. Despite these advancements, challenges remain regarding regulatory compliance, data privacy concerns, and disparities in access to diagnostic services. The report underscores the need for ongoing collaboration among stakeholders to address these limitations effectively.
EXPERT OPINION: By prioritizing equitable access and continuously evaluating emerging technologies' impact on patient safety and health outcomes, the healthcare system can harness the full potential of modern diagnostics to improve global health.
Additional Links: PMID-39957183
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PubMed:
Citation:
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@article {pmid39957183,
year = {2025},
author = {Weiskirchen, S and Weiskirchen, R},
title = {Unraveling the future: hot topics shaping molecular diagnostics Today.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2467969},
pmid = {39957183},
issn = {1744-8352},
abstract = {INTRODUCTION: This special report highlights the transformative potential of advanced diagnostic technologies in modern healthcare, emphasizing their role in enhancing disease detection, treatment personalization, and patient outcomes.
AREAS COVERED: Innovations such as Next-Generation Sequencing (NGS), liquid biopsy, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -based diagnostics, Point-of-Care (PoC) testing, microbiome analysis, and Artificial Intelligence are reshaping the diagnostic landscape. These methods facilitate early identification of diseases, enable tailored therapies based on individual genetic profiles, and provide noninvasive monitoring options. Furthermore, telemedicine enhances access to care while reducing costs associated with traditional healthcare delivery. Despite these advancements, challenges remain regarding regulatory compliance, data privacy concerns, and disparities in access to diagnostic services. The report underscores the need for ongoing collaboration among stakeholders to address these limitations effectively.
EXPERT OPINION: By prioritizing equitable access and continuously evaluating emerging technologies' impact on patient safety and health outcomes, the healthcare system can harness the full potential of modern diagnostics to improve global health.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Difference of the gut microbiota of premature ovarian insufficiency in two traditional Chinese syndromes.
Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan, 45(1):132-139.
PURPOSE: To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency (POI).
METHODS: Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020. Women with POI were divided into the kidney deficiency and blood stasis syndrome (SDBS) and Qi and blood deficiency syndrome (QBDS) groups. Gut microbial community profiles were analyzed by 16S rRNA gene sequencing using an Illumina MiSeq system. A retrospective study comparing hormone levels and gut microbiota information was performed between the SDBS and QBDS groups.
RESULTS: Compared with the QBDS group, the serum levels of estradiol (E2) and anti-Müllerian hormone (AMH) were significantly decreased in the SDBS group. The quantities of Adlercreutzia, Eggerthella, Klebsiella, and Paraprevotella significantly increased in the SDBS group, whereas Lactobacillus decreased significantly. Moreover, alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH. The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71.
CONCLUSIONS: There were significant differences in the dominant microbiota between the SDBS and QBDS groups, and the change in Proteobacteria in the QBDS group was more significant. The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups, which may provide a basis for the objectification of TCM syndrome types.
Additional Links: PMID-39957167
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PubMed:
Citation:
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@article {pmid39957167,
year = {2025},
author = {Jiaman, WU and Yan, N and Liya, T and Fei, MA and Yanting, L and Yuanyuan, Z},
title = {Difference of the gut microbiota of premature ovarian insufficiency in two traditional Chinese syndromes.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {1},
pages = {132-139},
doi = {10.19852/j.cnki.jtcm.2025.01.012},
pmid = {39957167},
issn = {2589-451X},
support = {SZZYSM202311010//Sanming Project of Medicine in Shenzhen: the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Luo Songping National Famous Chinese Medicine Practitioner Female Reproductive Disorders Prevention and Treatment Team/ ; 20181229//Guangdong Provincial Administration of Traditional Chinese Medicine: Investigation of the Mechanism of Regulating Ren-Tong-Du Acupuncture on Ovarian Granulosa Cells in Polycystic Ovary Syndrome based on Activin A /Smads Signalling Pathway/ ; 20201294//Guangdong Provincial Administration of Traditional Chinese Medicine: Evaluation of the Efficacy of Menstrual Regulation and Pregnancy Promotion by Acupuncture in the Treatment of Premature Ovarian Insufficiency/ ; JCYJ20210324130001004//Shenzhen Science and Innovation Commission: Investigating the Mechanism of Action of Acupuncture in Regulating the Gut Microbiome to Inhibit Apoptosis of Ovarian Granulosa Cells in Premature Ovarian Insufficiency Mice based on the Rictor/Torepamycin Target Protein C2 Pathway/ ; },
mesh = {Humans ; Female ; *Primary Ovarian Insufficiency/microbiology/blood/genetics ; *Gastrointestinal Microbiome ; Adult ; Young Adult ; Retrospective Studies ; *Bacteria/classification/isolation & purification/genetics ; Medicine, Chinese Traditional ; Anti-Mullerian Hormone/blood ; Estradiol/blood ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency (POI).
METHODS: Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020. Women with POI were divided into the kidney deficiency and blood stasis syndrome (SDBS) and Qi and blood deficiency syndrome (QBDS) groups. Gut microbial community profiles were analyzed by 16S rRNA gene sequencing using an Illumina MiSeq system. A retrospective study comparing hormone levels and gut microbiota information was performed between the SDBS and QBDS groups.
RESULTS: Compared with the QBDS group, the serum levels of estradiol (E2) and anti-Müllerian hormone (AMH) were significantly decreased in the SDBS group. The quantities of Adlercreutzia, Eggerthella, Klebsiella, and Paraprevotella significantly increased in the SDBS group, whereas Lactobacillus decreased significantly. Moreover, alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH. The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71.
CONCLUSIONS: There were significant differences in the dominant microbiota between the SDBS and QBDS groups, and the change in Proteobacteria in the QBDS group was more significant. The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups, which may provide a basis for the objectification of TCM syndrome types.},
}
MeSH Terms:
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hide MeSH Terms
Humans
Female
*Primary Ovarian Insufficiency/microbiology/blood/genetics
*Gastrointestinal Microbiome
Adult
Young Adult
Retrospective Studies
*Bacteria/classification/isolation & purification/genetics
Medicine, Chinese Traditional
Anti-Mullerian Hormone/blood
Estradiol/blood
RNA, Ribosomal, 16S/genetics
RevDate: 2025-02-16
CmpDate: 2025-02-16
Salivary microbiome profile shifts after scaling in stunted children.
BMC research notes, 18(1):69 pii:10.1186/s13104-025-07147-w.
OBJECTIVE: Stunting is a condition of impaired growth in children resulting from chronic malnutrition, characterized by shorter stature compared to peers of the same age. This condition leads to salivary gland dysfunction, which triggers oral dysbiosis and increases the risk of periodontal disease in children. Scaling and root planing (SRP) is the gold standard treatment for periodontal disease, aimed at reducing pathogenic bacterial populations. This study aimed to evaluate the effect of SRP treatment on the oral microbiome profile in the saliva of stunted children. A pre- and post-test study design was employed, involving 10 elementary school children divided into two groups: normal children and stunted children. Each participant underwent scaling, with saliva samples collected before and after the procedure. The oral microbiome profile was analyzed using next-generation sequencing, generating taxonomic data at the phylum, genus, and species level.
RESULT: Statistical analysis revealed significant changes in the gingival index, a clinical parameter, in the normal group but not in the stunted group. Scaling resulted in shifts in the microbiome profile in both groups, with the dominant phyla identified as Proteobacteria, Bacteroidota, and Firmicutes. Scaling procedure alters the oral microbiome profile in stunted children without affecting the clinical parameter.
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@article {pmid39956914,
year = {2025},
author = {Octaricha, T and Ilmiawati, C and Kasuma, N},
title = {Salivary microbiome profile shifts after scaling in stunted children.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {69},
doi = {10.1186/s13104-025-07147-w},
pmid = {39956914},
issn = {1756-0500},
support = {No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; },
mesh = {Humans ; *Saliva/microbiology ; Child ; *Microbiota ; Male ; Female ; *Growth Disorders/microbiology ; Dental Scaling/methods ; Periodontal Index ; },
abstract = {OBJECTIVE: Stunting is a condition of impaired growth in children resulting from chronic malnutrition, characterized by shorter stature compared to peers of the same age. This condition leads to salivary gland dysfunction, which triggers oral dysbiosis and increases the risk of periodontal disease in children. Scaling and root planing (SRP) is the gold standard treatment for periodontal disease, aimed at reducing pathogenic bacterial populations. This study aimed to evaluate the effect of SRP treatment on the oral microbiome profile in the saliva of stunted children. A pre- and post-test study design was employed, involving 10 elementary school children divided into two groups: normal children and stunted children. Each participant underwent scaling, with saliva samples collected before and after the procedure. The oral microbiome profile was analyzed using next-generation sequencing, generating taxonomic data at the phylum, genus, and species level.
RESULT: Statistical analysis revealed significant changes in the gingival index, a clinical parameter, in the normal group but not in the stunted group. Scaling resulted in shifts in the microbiome profile in both groups, with the dominant phyla identified as Proteobacteria, Bacteroidota, and Firmicutes. Scaling procedure alters the oral microbiome profile in stunted children without affecting the clinical parameter.},
}
MeSH Terms:
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hide MeSH Terms
Humans
*Saliva/microbiology
Child
*Microbiota
Male
Female
*Growth Disorders/microbiology
Dental Scaling/methods
Periodontal Index
RevDate: 2025-02-17
Bile acid receptors and signaling crosstalk in the liver, gut and brain.
Liver research, 5(3):105-118.
Bile acids are physiological detergents derived from cholesterol that aid in digestion and nutrient absorption, and they play roles in glucose, lipid, and energy metabolism and in gut microbiome and metabolic homeostasis. Bile acids mediate crosstalk between the liver and gut through bactericidal modulation of the gut microbiome, while gut microbes influence the composition of the circulating bile acid pool. Recent research indicates bile acids may also be important mediators of neurological disease by acting as peripheral signaling molecules that activate bile acid receptors in the blood-brain barrier and in the brain itself. This review highlights the role of bile acids in maintaining liver and gut microbe homeostasis, as well as their function as mediators of cellular signaling in the liver-gut-brain axis.
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@article {pmid39957847,
year = {2021},
author = {Ferrell, JM and Chiang, JYL},
title = {Bile acid receptors and signaling crosstalk in the liver, gut and brain.},
journal = {Liver research},
volume = {5},
number = {3},
pages = {105-118},
pmid = {39957847},
issn = {2542-5684},
abstract = {Bile acids are physiological detergents derived from cholesterol that aid in digestion and nutrient absorption, and they play roles in glucose, lipid, and energy metabolism and in gut microbiome and metabolic homeostasis. Bile acids mediate crosstalk between the liver and gut through bactericidal modulation of the gut microbiome, while gut microbes influence the composition of the circulating bile acid pool. Recent research indicates bile acids may also be important mediators of neurological disease by acting as peripheral signaling molecules that activate bile acid receptors in the blood-brain barrier and in the brain itself. This review highlights the role of bile acids in maintaining liver and gut microbe homeostasis, as well as their function as mediators of cellular signaling in the liver-gut-brain axis.},
}
RevDate: 2025-02-16
Cyanobacteria microbiomes for bioplastic production: Critical review of key factors and challenges in scaling from laboratory to industry set-ups.
Bioresource technology pii:S0960-8524(25)00197-X [Epub ahead of print].
Cyanobacteria are photoautotrophic microorganisms capable of accumulating polyhydroxybutyrate (PHB). A novel approach for PHB production involves the exploration of cyanobacterial microbiomes, potentially reducing costs through non-sterile cultivation with non-pure substrates. Although still in its early stages, this approach shows promise for high yields and sustained synthesis. However, managing microbiome population dynamics in non-sterile environments requires effective monitoring and control. This review covers PHB production by cyanobacteria microbiomes, from sample procurement to laboratory-scale production. It highlights recent insights into optimizing cultivation parameters for enhanced biopolymer yield. Strategies to overcome challenges in PHB production are evaluated, emphasizing integrated molecular biology techniques with quantitative and qualitative PHB analysis. Finally, key challenges in scaling up production to industrial-scale scenarios are discussed, along with potential solutions to support the development of sustainable industrial processes. Cyanobacteria microbiomes show promise PHB production but challenges like managing non-sterile conditions and scaling up require optimized strategies and integrated approaches.
Additional Links: PMID-39956522
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PubMed:
Citation:
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@article {pmid39956522,
year = {2025},
author = {Altamira-Algarra, B and Garcia, J and Gonzalez-Flo, E},
title = {Cyanobacteria microbiomes for bioplastic production: Critical review of key factors and challenges in scaling from laboratory to industry set-ups.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132231},
doi = {10.1016/j.biortech.2025.132231},
pmid = {39956522},
issn = {1873-2976},
abstract = {Cyanobacteria are photoautotrophic microorganisms capable of accumulating polyhydroxybutyrate (PHB). A novel approach for PHB production involves the exploration of cyanobacterial microbiomes, potentially reducing costs through non-sterile cultivation with non-pure substrates. Although still in its early stages, this approach shows promise for high yields and sustained synthesis. However, managing microbiome population dynamics in non-sterile environments requires effective monitoring and control. This review covers PHB production by cyanobacteria microbiomes, from sample procurement to laboratory-scale production. It highlights recent insights into optimizing cultivation parameters for enhanced biopolymer yield. Strategies to overcome challenges in PHB production are evaluated, emphasizing integrated molecular biology techniques with quantitative and qualitative PHB analysis. Finally, key challenges in scaling up production to industrial-scale scenarios are discussed, along with potential solutions to support the development of sustainable industrial processes. Cyanobacteria microbiomes show promise PHB production but challenges like managing non-sterile conditions and scaling up require optimized strategies and integrated approaches.},
}
RevDate: 2025-02-16
Autoimmunity in Long-COVID.
The Journal of allergy and clinical immunology pii:S0091-6749(25)00171-X [Epub ahead of print].
Long-COVID (also termed Post-Acute Sequelae of SARS-CoV-2 or PASC) affects up to 10% of people recovering from SARS-CoV-2 infection. Diagnosis is hampered by diffuse symptomatology, lack of biomarkers, an incomplete understanding of pathogenesis, and the lack of validated treatments. In terms of pathogenesis, hypothesised causes include viral persistence, the legacy of endotheliitis and thrombosis, low-grade tissue-based inflammation and/or scarring, perturbation of the host virome/microbiome, or triggering of autoimmunity. Several studies show pre-existing and/or de novo production of autoantibodies after infection with SARS-CoV-2, but the persistence of these antibodies and their role in causing long-COVID is debated. Here, we review the mechanisms through which autoimmune responses can arise during and after viral infection, focusing on the evidence for B-cell dysregulation and autoantibody production in acute and long-COVID.
Additional Links: PMID-39956285
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@article {pmid39956285,
year = {2025},
author = {Talwar, S and Harker, JA and Openshaw, PJM and Thwaites, RS},
title = {Autoimmunity in Long-COVID.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.02.005},
pmid = {39956285},
issn = {1097-6825},
abstract = {Long-COVID (also termed Post-Acute Sequelae of SARS-CoV-2 or PASC) affects up to 10% of people recovering from SARS-CoV-2 infection. Diagnosis is hampered by diffuse symptomatology, lack of biomarkers, an incomplete understanding of pathogenesis, and the lack of validated treatments. In terms of pathogenesis, hypothesised causes include viral persistence, the legacy of endotheliitis and thrombosis, low-grade tissue-based inflammation and/or scarring, perturbation of the host virome/microbiome, or triggering of autoimmunity. Several studies show pre-existing and/or de novo production of autoantibodies after infection with SARS-CoV-2, but the persistence of these antibodies and their role in causing long-COVID is debated. Here, we review the mechanisms through which autoimmune responses can arise during and after viral infection, focusing on the evidence for B-cell dysregulation and autoantibody production in acute and long-COVID.},
}
RevDate: 2025-02-16
Cubebin alleviates chronic stress-induced depression-like behavior in mice by regulating the gut microbiome.
European journal of pharmacology pii:S0014-2999(25)00138-4 [Epub ahead of print].
The gut-brain axis is dysregulated as a consequence of alterations in the gut microbiota. These alterations increase toxic microbial metabolites, endotoxemia, and the release of immune mediators and contribute to the development of depression. Cubebin is a dibenzyl butyrolactone lignan, and its stem is also known as Agaru in Tibetan areas, it is commonly used as a sedative and tranquilizing medicine. This study aimed to investigate the effects of cubebin on chronic stress-induced depression-like behavior in mice. Cubebin was observed to mitigate depressive-like behavior in chronic unpredictable mild stress (CUMS) mice, influence the restoration of their cerebral cortex and hippocampal tissue morphology, and enhance the abundance of relevant intestinal flora in depression model mice, particularly by decreasing the abundance of Clostridium, Dorea, and Ruminococcus. The final protein function expression was normalized by regulating depression-related metabolic pathways. Concomitantly, the concentrations of neurotransmitters serotonin (5-HT), norepinephrine (NE), and dopamine (DA) in the brains of mice in the model group were enhanced, and their depressive symptoms were mitigated. Our study findings suggest that cubebin may ameliorate CUMS-induced depression in mice by modulating the microbe-gut-brain axis, elucidating the key effect of gut metabolites on depressive symptoms.
Additional Links: PMID-39956262
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@article {pmid39956262,
year = {2025},
author = {Wan, M and Wang, W and He, M and Yang, S and Feng, Y and Luo, Y},
title = {Cubebin alleviates chronic stress-induced depression-like behavior in mice by regulating the gut microbiome.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {177384},
doi = {10.1016/j.ejphar.2025.177384},
pmid = {39956262},
issn = {1879-0712},
abstract = {The gut-brain axis is dysregulated as a consequence of alterations in the gut microbiota. These alterations increase toxic microbial metabolites, endotoxemia, and the release of immune mediators and contribute to the development of depression. Cubebin is a dibenzyl butyrolactone lignan, and its stem is also known as Agaru in Tibetan areas, it is commonly used as a sedative and tranquilizing medicine. This study aimed to investigate the effects of cubebin on chronic stress-induced depression-like behavior in mice. Cubebin was observed to mitigate depressive-like behavior in chronic unpredictable mild stress (CUMS) mice, influence the restoration of their cerebral cortex and hippocampal tissue morphology, and enhance the abundance of relevant intestinal flora in depression model mice, particularly by decreasing the abundance of Clostridium, Dorea, and Ruminococcus. The final protein function expression was normalized by regulating depression-related metabolic pathways. Concomitantly, the concentrations of neurotransmitters serotonin (5-HT), norepinephrine (NE), and dopamine (DA) in the brains of mice in the model group were enhanced, and their depressive symptoms were mitigated. Our study findings suggest that cubebin may ameliorate CUMS-induced depression in mice by modulating the microbe-gut-brain axis, elucidating the key effect of gut metabolites on depressive symptoms.},
}
RevDate: 2025-02-16
CmpDate: 2025-02-16
Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.
Environmental microbiology, 27(2):e70056.
Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.
Additional Links: PMID-39956110
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@article {pmid39956110,
year = {2025},
author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU},
title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70056},
doi = {10.1111/1462-2920.70056},
pmid = {39956110},
issn = {1462-2920},
support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; },
abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.},
}
MeSH Terms:
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*Methane/metabolism
*Geologic Sediments/microbiology
*Bioreactors/microbiology
*Sulfides/metabolism
Sweden
*Nitrogen/metabolism
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Archaea/metabolism/genetics/classification
Seawater/microbiology
Bacteria/classification/genetics/metabolism
Oxidation-Reduction
Denitrification
Nitrates/metabolism
Phylogeny
Ecosystem
RevDate: 2025-02-16
Insights into high ammonia-resistant syntrophic microbiomes and metabolic pathways during continuous anaerobic digestion of cow manure.
Bioresource technology pii:S0960-8524(25)00201-9 [Epub ahead of print].
Understanding microbial responses to ammonia is critical for defining thresholds and ensuring stable operation of anaerobic digestion (AD); however, an understanding of the microbiome's resistance mechanisms to high-total-ammonia-nitrogen (TAN) conditions remains limited. This study determined a TAN threshold of 7 g/L for continuous cow manure AD with increasing TAN levels. TAN was identified as the most critical factor influencing the AD performance, with CH4 production decreasing by > 50 % beyond this level. Additionally, a highly TAN-resistant syntrophic microbiome was identified through network analysis, highlighting key bacteria, Thauera phenolivorans and Fermentimons spp., alongside hydrogenotrophic methanogens. Interestingly, shifts were observed within the hydrogenotrophic methanogen community, transitioning from Methanoculleus bourgensis to Methanoculleus chikugoensis, Methanocorpusculum spp. and Methanobacterium spp. under high-TAN conditions. Significant metabolic pathways specific to high-TAN environments were identified, providing insights into their roles in sustained operation of AD. These findings highlight the performance limitations and functional redundancy under high-TAN conditions.
Additional Links: PMID-39956519
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@article {pmid39956519,
year = {2025},
author = {Bae, I and Rhee, C and Shin, J and Cho, K and Triolo, JM and Shin, SG},
title = {Insights into high ammonia-resistant syntrophic microbiomes and metabolic pathways during continuous anaerobic digestion of cow manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132235},
doi = {10.1016/j.biortech.2025.132235},
pmid = {39956519},
issn = {1873-2976},
abstract = {Understanding microbial responses to ammonia is critical for defining thresholds and ensuring stable operation of anaerobic digestion (AD); however, an understanding of the microbiome's resistance mechanisms to high-total-ammonia-nitrogen (TAN) conditions remains limited. This study determined a TAN threshold of 7 g/L for continuous cow manure AD with increasing TAN levels. TAN was identified as the most critical factor influencing the AD performance, with CH4 production decreasing by > 50 % beyond this level. Additionally, a highly TAN-resistant syntrophic microbiome was identified through network analysis, highlighting key bacteria, Thauera phenolivorans and Fermentimons spp., alongside hydrogenotrophic methanogens. Interestingly, shifts were observed within the hydrogenotrophic methanogen community, transitioning from Methanoculleus bourgensis to Methanoculleus chikugoensis, Methanocorpusculum spp. and Methanobacterium spp. under high-TAN conditions. Significant metabolic pathways specific to high-TAN environments were identified, providing insights into their roles in sustained operation of AD. These findings highlight the performance limitations and functional redundancy under high-TAN conditions.},
}
RevDate: 2025-02-16
Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.
The Journal of biological chemistry pii:S0021-9258(25)00168-1 [Epub ahead of print].
The production of short-chain fatty acids (SCFAs) by Firmicutes (Bacillota) within the human gastrointestinal tract is recognized as critical for gut health and the progression of a range of disease states. Firmicutes are the most diverse phylum of human gut bacteria and are highly studied, and are often specialized to degrade just a few polysaccharide substrates. Members of the Firmicutes include key bacteria that produce butyrate, an SCFA that is generally not produced by members of the other major phyla. Recently, it was shown that Eubacterium rectale, a widespread member of the Firmicutes belonging to the Clostridiales cluster XIVa, can grow on the unusual but ubiquitous plant-derived sugar SQ using a sulfoglycolytic sulfofructose transaldolase pathway. Here, we show that in addition to SQ, E. rectale can also grow on the SQ glycoside sulfoquinovosyl glycerol (SQGro). The 3D structure of the E. rectale sulfoquinovosidase (SftG) shares strong structural conservation with other carbohydrate active enzyme family GH31 SQases. Using sequence-similarity networks, we provide new biological context to a conserved domain of unknown function protein SftX belonging to DUF4867, which is conserved in the sulfoglycolytic sulfofructose transaldolase pathway, and determine its 3D structure. Finally, with the aid of a synthetic mini-human microbiome reconstituted in germ-free mice, we show that an SQ dietary supplement can rescue E. rectale from population crashes that occur upon switching from a high-fiber to a low-fiber, high-fat diet. This suggests that SQ or SQGro has potential as a prebiotic for promoting the maintenance of this important butyrate-producing bacterium within the colonic microbiota.
Additional Links: PMID-39956340
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@article {pmid39956340,
year = {2025},
author = {Sharma, M and Pudlo, N and Järvå, MA and Kaur, A and John, A and Burchill, L and Lingford, JP and Epa, R and Abayakoon, P and Scott, NE and Turkenburg, JP and Davies, GJ and Martens, EC and Goddard-Borger, ED and Williams, SJ},
title = {Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {108320},
doi = {10.1016/j.jbc.2025.108320},
pmid = {39956340},
issn = {1083-351X},
abstract = {The production of short-chain fatty acids (SCFAs) by Firmicutes (Bacillota) within the human gastrointestinal tract is recognized as critical for gut health and the progression of a range of disease states. Firmicutes are the most diverse phylum of human gut bacteria and are highly studied, and are often specialized to degrade just a few polysaccharide substrates. Members of the Firmicutes include key bacteria that produce butyrate, an SCFA that is generally not produced by members of the other major phyla. Recently, it was shown that Eubacterium rectale, a widespread member of the Firmicutes belonging to the Clostridiales cluster XIVa, can grow on the unusual but ubiquitous plant-derived sugar SQ using a sulfoglycolytic sulfofructose transaldolase pathway. Here, we show that in addition to SQ, E. rectale can also grow on the SQ glycoside sulfoquinovosyl glycerol (SQGro). The 3D structure of the E. rectale sulfoquinovosidase (SftG) shares strong structural conservation with other carbohydrate active enzyme family GH31 SQases. Using sequence-similarity networks, we provide new biological context to a conserved domain of unknown function protein SftX belonging to DUF4867, which is conserved in the sulfoglycolytic sulfofructose transaldolase pathway, and determine its 3D structure. Finally, with the aid of a synthetic mini-human microbiome reconstituted in germ-free mice, we show that an SQ dietary supplement can rescue E. rectale from population crashes that occur upon switching from a high-fiber to a low-fiber, high-fat diet. This suggests that SQ or SQGro has potential as a prebiotic for promoting the maintenance of this important butyrate-producing bacterium within the colonic microbiota.},
}
RevDate: 2025-02-16
A Mediterranean diet for Crohn's disease: Embracing colorful diversity to improve the microbiome.
Additional Links: PMID-39956335
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@article {pmid39956335,
year = {2025},
author = {Abreu, MT and Devkota, S and Issokson, K},
title = {A Mediterranean diet for Crohn's disease: Embracing colorful diversity to improve the microbiome.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.02.003},
pmid = {39956335},
issn = {1528-0012},
}
RevDate: 2025-02-16
TREM2 depletion in pancreatic cancer elicits pathogenic inflammation and accelerates tumor progression via enriching IL-1β[+] macrophages.
Gastroenterology pii:S0016-5085(25)00368-3 [Epub ahead of print].
BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) has a complex tumor microenvironment enriched with tumor-associated macrophages. Triggering receptor expressed on myeloid cells 2 (TREM2) is highly expressed by a subset of macrophages in PDAC. However, the functional role of TREM2 in PDAC progression remains elusive.
METHODS: We generated a novel transgenic mouse model (KPPC;Trem2[-/-]) that enables the genetic depletion of TREM2 in the context of spontaneous PDAC development. Single-cell RNA-sequencing analysis was utilized to identify changes in the tumor immune microenvironment upon TREM2 depletion. We evaluated the impacts of TREM2 depletion on the tumor immune microenvironment to elucidate the functions of TREM2 in macrophages and PDAC development.
RESULTS: Unexpectedly, genetic depletion of TREM2 significantly accelerated spontaneous PDAC progression and shortened the survival of KPPC;Trem2[-/-] mice. Single-cell analysis revealed that TREM2 depletion enhanced pro-inflammatory macrophages and exacerbated pathogenic inflammation in PDAC. Specifically, TREM2 functions as a key braking mechanism for the NLRP3/NF-κB/IL-1β inflammasome pathway, opposing to microbial lipopolysaccharide (LPS) as the key activator of this pathway. TREM2 deficiency orchestrated with microbial LPS to trigger IL-1β upregulation and pathogenic inflammation, thereby fueling PDAC development. Notably, IL-1β inhibition or microbiome ablation not only reversed the accelerated PDAC progression caused by TREM2 depletion, but also further inhibited PDAC progression in the TREM2-depleted context.
CONCLUSIONS: TREM2 depletion accelerates tumor progression by enhancing pro-inflammatory macrophages and IL-1β-mediated pathogenic inflammation in PDAC. The accelerated tumor progression by TREM2 depletion can be reversed by blocking IL-1β-associated pathogenic inflammation.
Additional Links: PMID-39956331
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@article {pmid39956331,
year = {2025},
author = {Yang, D and Sun, X and Wang, H and Wistuba, II and Wang, H and Maitra, A and Chen, Y},
title = {TREM2 depletion in pancreatic cancer elicits pathogenic inflammation and accelerates tumor progression via enriching IL-1β[+] macrophages.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.01.244},
pmid = {39956331},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Pancreatic ductal adenocarcinoma (PDAC) has a complex tumor microenvironment enriched with tumor-associated macrophages. Triggering receptor expressed on myeloid cells 2 (TREM2) is highly expressed by a subset of macrophages in PDAC. However, the functional role of TREM2 in PDAC progression remains elusive.
METHODS: We generated a novel transgenic mouse model (KPPC;Trem2[-/-]) that enables the genetic depletion of TREM2 in the context of spontaneous PDAC development. Single-cell RNA-sequencing analysis was utilized to identify changes in the tumor immune microenvironment upon TREM2 depletion. We evaluated the impacts of TREM2 depletion on the tumor immune microenvironment to elucidate the functions of TREM2 in macrophages and PDAC development.
RESULTS: Unexpectedly, genetic depletion of TREM2 significantly accelerated spontaneous PDAC progression and shortened the survival of KPPC;Trem2[-/-] mice. Single-cell analysis revealed that TREM2 depletion enhanced pro-inflammatory macrophages and exacerbated pathogenic inflammation in PDAC. Specifically, TREM2 functions as a key braking mechanism for the NLRP3/NF-κB/IL-1β inflammasome pathway, opposing to microbial lipopolysaccharide (LPS) as the key activator of this pathway. TREM2 deficiency orchestrated with microbial LPS to trigger IL-1β upregulation and pathogenic inflammation, thereby fueling PDAC development. Notably, IL-1β inhibition or microbiome ablation not only reversed the accelerated PDAC progression caused by TREM2 depletion, but also further inhibited PDAC progression in the TREM2-depleted context.
CONCLUSIONS: TREM2 depletion accelerates tumor progression by enhancing pro-inflammatory macrophages and IL-1β-mediated pathogenic inflammation in PDAC. The accelerated tumor progression by TREM2 depletion can be reversed by blocking IL-1β-associated pathogenic inflammation.},
}
RevDate: 2025-02-16
Salting-out assisted liquid-liquid extraction for UPLC-MS/MS determination of bile acids and kynurenine-, indole- and serotonin-pathway metabolites of tryptophan in human serum of healthy probands.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 1255:124519 pii:S1570-0232(25)00071-6 [Epub ahead of print].
The bacterial composition of the gut has been found to affect many diseases, including several gastrointestinal cancers. The microbiome appears central in the production of certain metabolites that enter circulation, especially those from bile acids and the essential amino acid tryptophan. The tumor-microenvironment may also produce changes in metabolites, such as those from the tryptophan-kynurenine pathway, of which several compounds may be measured in the blood. As data emerges from large scale metabolomics studies, there will be a need to validate metabolomic biomarkers to confirm their clinical utility. This task also requires knowledge about biological variation of the same metabolites in a healthy population. For this purpose, a novel method was developed for quantification of bile acids and tryptophan metabolites in samples of human serum by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Salting-out assisted liquid-liquid extraction was optimized with the ion-pairing reagent trifluoroacetic acid. In this way, both polar tryptophan metabolites and non-polar bile acids could be extracted with a high recovery, favorable matrix effects, and improved chromatographic focusing, by using straightforward robot pipetting. The instrumental analysis was fast (4 min and 32 s) and with sample injections done directly from the extraction microplate. The method was applied to quantify metabolites in serum from healthy probands, and for investigating inter- and intraindividual variations over six hours.
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@article {pmid39955961,
year = {2025},
author = {Oanes, C and Alexeeva, M and Søreide, K and Brede, C},
title = {Salting-out assisted liquid-liquid extraction for UPLC-MS/MS determination of bile acids and kynurenine-, indole- and serotonin-pathway metabolites of tryptophan in human serum of healthy probands.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1255},
number = {},
pages = {124519},
doi = {10.1016/j.jchromb.2025.124519},
pmid = {39955961},
issn = {1873-376X},
abstract = {The bacterial composition of the gut has been found to affect many diseases, including several gastrointestinal cancers. The microbiome appears central in the production of certain metabolites that enter circulation, especially those from bile acids and the essential amino acid tryptophan. The tumor-microenvironment may also produce changes in metabolites, such as those from the tryptophan-kynurenine pathway, of which several compounds may be measured in the blood. As data emerges from large scale metabolomics studies, there will be a need to validate metabolomic biomarkers to confirm their clinical utility. This task also requires knowledge about biological variation of the same metabolites in a healthy population. For this purpose, a novel method was developed for quantification of bile acids and tryptophan metabolites in samples of human serum by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Salting-out assisted liquid-liquid extraction was optimized with the ion-pairing reagent trifluoroacetic acid. In this way, both polar tryptophan metabolites and non-polar bile acids could be extracted with a high recovery, favorable matrix effects, and improved chromatographic focusing, by using straightforward robot pipetting. The instrumental analysis was fast (4 min and 32 s) and with sample injections done directly from the extraction microplate. The method was applied to quantify metabolites in serum from healthy probands, and for investigating inter- and intraindividual variations over six hours.},
}
RevDate: 2025-02-16
Dysbiosis involving methionine and PPAR-γ pathways is associated with early onset atopic dermatitis and food allergy.
Asian Pacific journal of allergy and immunology [Epub ahead of print].
BACKGROUND: Atopic dermatitis (AD) and food allergy (FA) often originate early in life. Gut microbiota interactions with the host immune system influence allergy development, yet the distinct gut microbiome and functional profiles in individuals with AD, FA, or both AD+FA remain underexplored.
OBJECTIVE: We investigated microbial colonization and proteomic profiles in infants with AD, FA, and AD+FA compared to age- and sex-matched controls from the Allergy Development in Early Life and Associated Factors in the Thai Birth Cohort (ALICE).
METHODS: Gut microbiomes from stool samples were analyzed using 16S sequencing, and proteomic analysis was conducted by liquid chromatography-tandem mass spectrometry.
RESULTS: The study included 16 AD, 5 FA, 5 AD+FA subjects, and 26 controls. AD+FA group exhibited the most severe dysbiosis. Enrichment of proteins involved in methionine biosynthesis in Bifidobacterium scardovii and high Erysipelotrichaceae colonization suggest a link to high-fat diets, known to reduce intestinal short-chain fatty acid and serotonin levels, contributing to allergies. Erysipelotrichaceae in AD+FA groups also expressed proteins related to histidine degradation. Low Bifidobacteriaceae levels were noted in FA and AD+FA, with more pathogenic strains colonized. Increased Bacteroidaceae in FA and AD+FA and Enterobacteriaceae in FA were detected. Pathways involving vitamin B1, a ligand for proliferator-activated receptor-γ (PPAR-γ) from Enterobacteriaceae could promote TH2 cells, type 2 innate lymphoid cells, and M2 macrophages, likely contribute to allergic inflammation.
CONCLUSIONS: AD+FA phenotype exhibited the most distinctive gut microbiome alterations, highlighting unique dysbiosis patterns. Microbiome biosynthesis pathways involving metabolism of methionine, histidine, serotonin, and vitamin B1 point to new targets for modifying or treating AD and FA.
Additional Links: PMID-39955638
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@article {pmid39955638,
year = {2025},
author = {Senavonge, A and Nakphaichit, M and Vongsangnak, W and Roytrakul, S and Patumcharoenpol, P and Kingkaw, A and Wongoutong, C and Weerapakorn, W and Pornputtapong, N and La-Ongkham, O and Poovorawan, Y and Wanlapakorn, N and Kittipongpattana, P and Nitisinprasert, S and Chatchatee, P and Suratannon, N},
title = {Dysbiosis involving methionine and PPAR-γ pathways is associated with early onset atopic dermatitis and food allergy.},
journal = {Asian Pacific journal of allergy and immunology},
volume = {},
number = {},
pages = {},
doi = {10.12932/AP-131223-1749},
pmid = {39955638},
issn = {0125-877X},
abstract = {BACKGROUND: Atopic dermatitis (AD) and food allergy (FA) often originate early in life. Gut microbiota interactions with the host immune system influence allergy development, yet the distinct gut microbiome and functional profiles in individuals with AD, FA, or both AD+FA remain underexplored.
OBJECTIVE: We investigated microbial colonization and proteomic profiles in infants with AD, FA, and AD+FA compared to age- and sex-matched controls from the Allergy Development in Early Life and Associated Factors in the Thai Birth Cohort (ALICE).
METHODS: Gut microbiomes from stool samples were analyzed using 16S sequencing, and proteomic analysis was conducted by liquid chromatography-tandem mass spectrometry.
RESULTS: The study included 16 AD, 5 FA, 5 AD+FA subjects, and 26 controls. AD+FA group exhibited the most severe dysbiosis. Enrichment of proteins involved in methionine biosynthesis in Bifidobacterium scardovii and high Erysipelotrichaceae colonization suggest a link to high-fat diets, known to reduce intestinal short-chain fatty acid and serotonin levels, contributing to allergies. Erysipelotrichaceae in AD+FA groups also expressed proteins related to histidine degradation. Low Bifidobacteriaceae levels were noted in FA and AD+FA, with more pathogenic strains colonized. Increased Bacteroidaceae in FA and AD+FA and Enterobacteriaceae in FA were detected. Pathways involving vitamin B1, a ligand for proliferator-activated receptor-γ (PPAR-γ) from Enterobacteriaceae could promote TH2 cells, type 2 innate lymphoid cells, and M2 macrophages, likely contribute to allergic inflammation.
CONCLUSIONS: AD+FA phenotype exhibited the most distinctive gut microbiome alterations, highlighting unique dysbiosis patterns. Microbiome biosynthesis pathways involving metabolism of methionine, histidine, serotonin, and vitamin B1 point to new targets for modifying or treating AD and FA.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Investigating the causal relationship between the gut microbiome and rheumatoid arthritis: mediating effects of immune cells.
Journal of translational medicine, 23(1):187.
BACKGROUND: Rheumatoid arthritis (RA) is a complex autoimmune and inflammatory disease that significantly impacts the quality of life for millions worldwide. In recent years, gut microbiota has garnered extensive attention as a potential health-modulating factor, with associations identified between it and various diseases, including RA. This study aims to investigate the causal relationship between gut microbiota and RA using Mendelian Randomization (MR) analysis, and further examines the mediating role of immune cells in this connection.
METHOD: A MR analytical method was employed by us, integrating genome-wide association study (GWAS) data from FinnGen, MiBioGen, and research led by Valeria Orrù and her team to systematically examine the relationships between gut microbiota, immune cells, and RA. Initially, we performed a bidirectional univariable MR analysis to examine the relationship between gut microbiota and RA, consciously avoiding any possible reverse causal influences. Following this, we applied multivariable MR adjustments on gut microbiota that showed positive associations and employed a two-step methodology to examine the overall genetic predictive role of immune cell-mediated gut microbiota in the risk of developing RA.
RESULT: Our results demonstrate notable causal connections between different gut microbiota and RA. In particular, Mollicutes, Ruminococcaceae UCG002, and Butyricimonas displayed positive associations with RA, while other microbiota, including Rikenellaceae, Lactobacillaceae, and Veillonella, showed negative associations. Additionally, we identified a reduction in the abundance of certain microbiota, including Lachnospiraceae and Ruminococcus1, which were excluded from our study and validated for analytical accuracy using methods such as "leave-one-out." Immune cells, including CD3 found on activated CD4 regulatory T cells that express CD39, serve a mediating function in the development of RA. To summarize, our research focused on the species Butyricimonas id. 945, recognizing immune cells as crucial contributors to the relationship between genetic predictions of gut microbiota and RA.
CONCLUSION: This research clarifies the intricate causal links between gut microbiota and RA, emphasizing the crucial mediating function of immune cells in this mechanism. These findings not only enhance our understanding of the pathogenesis of RA but also provide new perspectives and potential intervention targets for future prevention and treatment strategies. Future research should further investigate the specific mechanisms underlying the interactions among gut microbiota, immune cells, and RA, while considering the validation of these findings across diverse populations.
Additional Links: PMID-39955590
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@article {pmid39955590,
year = {2025},
author = {Lan, W and Lu, Q and Ma, W and Jiang, Z and Chen, Y and Wang, Z and Yao, X and Tang, F},
title = {Investigating the causal relationship between the gut microbiome and rheumatoid arthritis: mediating effects of immune cells.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {187},
pmid = {39955590},
issn = {1479-5876},
support = {[2023]435//Science and Technology Program of Guizhou Province (Guizhou Scientific Foundation-Platform and talent/ ; 82160917//National Natural Science Foundation of China/ ; 2022]004//Guizhou University of Traditional Chinese Medicine National and Provincial Science and Technology Innovation Talent Team Cultivation Project (Guizhou University of Traditional Chinese Medicine TD NO/ ; },
mesh = {*Arthritis, Rheumatoid/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Causality ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a complex autoimmune and inflammatory disease that significantly impacts the quality of life for millions worldwide. In recent years, gut microbiota has garnered extensive attention as a potential health-modulating factor, with associations identified between it and various diseases, including RA. This study aims to investigate the causal relationship between gut microbiota and RA using Mendelian Randomization (MR) analysis, and further examines the mediating role of immune cells in this connection.
METHOD: A MR analytical method was employed by us, integrating genome-wide association study (GWAS) data from FinnGen, MiBioGen, and research led by Valeria Orrù and her team to systematically examine the relationships between gut microbiota, immune cells, and RA. Initially, we performed a bidirectional univariable MR analysis to examine the relationship between gut microbiota and RA, consciously avoiding any possible reverse causal influences. Following this, we applied multivariable MR adjustments on gut microbiota that showed positive associations and employed a two-step methodology to examine the overall genetic predictive role of immune cell-mediated gut microbiota in the risk of developing RA.
RESULT: Our results demonstrate notable causal connections between different gut microbiota and RA. In particular, Mollicutes, Ruminococcaceae UCG002, and Butyricimonas displayed positive associations with RA, while other microbiota, including Rikenellaceae, Lactobacillaceae, and Veillonella, showed negative associations. Additionally, we identified a reduction in the abundance of certain microbiota, including Lachnospiraceae and Ruminococcus1, which were excluded from our study and validated for analytical accuracy using methods such as "leave-one-out." Immune cells, including CD3 found on activated CD4 regulatory T cells that express CD39, serve a mediating function in the development of RA. To summarize, our research focused on the species Butyricimonas id. 945, recognizing immune cells as crucial contributors to the relationship between genetic predictions of gut microbiota and RA.
CONCLUSION: This research clarifies the intricate causal links between gut microbiota and RA, emphasizing the crucial mediating function of immune cells in this mechanism. These findings not only enhance our understanding of the pathogenesis of RA but also provide new perspectives and potential intervention targets for future prevention and treatment strategies. Future research should further investigate the specific mechanisms underlying the interactions among gut microbiota, immune cells, and RA, while considering the validation of these findings across diverse populations.},
}
MeSH Terms:
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*Arthritis, Rheumatoid/microbiology/immunology
Humans
*Gastrointestinal Microbiome
Genome-Wide Association Study
Mendelian Randomization Analysis
Causality
RevDate: 2025-02-15
CmpDate: 2025-02-15
Associations of the gut, cervical, and vaginal microbiota with cervical cancer: a systematic review and meta-analysis.
BMC women's health, 25(1):65.
BACKGROUND: An increasing number of studies indicate that the gut, cervical, and vaginal microbiota may play crucial roles in the development of cervical cancer (CC). However, the interactions between the microbiota and the host are yet unknown. To address this gap, a systematic review and meta-analysis were conducted to assess the microbiota alterations in a variety of body locations, including the gut and genital tract.
METHODS: Electronic searches of PubMed, Embase, Web of Science, and the Cochrane Library were conducted to retrieve eligible papers published from January 1, 2014, to January 1, 2024 (PROSPERO: CRD42024554433). This study was restricted to English-language studies reporting on alpha diversity, beta diversity, and relative abundance, as well as on patients with CC whose microbiota had been analyzed via next-generation sequencing technologies. To assess the risk of bias (RoB), we utilized the Newcastle‒Ottawa Quality Assessment Scale (NOS) and the ROBINS-I tool. For the meta-analysis, we employed Review Manager 5.4.
RESULTS: Thirty-six eligible studies were included in this review. The Chao1 index (SMD = 0.96, [95% CI: 0.71, 1.21], I[2] = 0%) and the Shannon index (SMD = 1.02, [95% CI: 0.53, 1.50], I[2] = 85%) values from vaginal samples were significantly greater in patients than in the controls. In the cervical samples, the Shannon index value (SMD = 1.29, [95% CI: 0.61, 1.97], I[2] = 93%) significantly increased, whereas the Chao1 index value did not significantly differ (SMD = 0.50, [95% CI: -0.46, 1.46], I[2] = 89%). The Shannon index value (SMD = 0.25, [95% CI: -0.22, 0.72], I[2] = 38%) did not significantly differ across the gut samples. The majority of studies (19/25) indicated that the patients and noncancer controls differed significantly in terms of beta diversity. Cancer-associated changes were observed, with a dramatic decrease in the Lactobacillus genus and significant increases in pathogenic bacteria, including the Anaerococcus, Peptostreptococcus, Porphyromonas, Prevotella, and Sneathia genera. Additionally, the impact of antineoplastic therapies on microbial diversity was inconsistently reported across several studies.
CONCLUSION: This systematic review elucidates the microbiota alterations associated with the prevalence of CC and its response to anti-tumor therapies, aiming to provide insights for future research directions and precision medicine strategies to enhance women's quality of life.
PROSPERO REGISTRATION: CRD42024554433.
Additional Links: PMID-39955550
PubMed:
Citation:
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@article {pmid39955550,
year = {2025},
author = {Wen, Q and Wang, S and Min, Y and Liu, X and Fang, J and Lang, J and Chen, M},
title = {Associations of the gut, cervical, and vaginal microbiota with cervical cancer: a systematic review and meta-analysis.},
journal = {BMC women's health},
volume = {25},
number = {1},
pages = {65},
pmid = {39955550},
issn = {1472-6874},
support = {2024-YF05-02230-SN//Chengdu Science and Technology Bureau/ ; 2024-803//Health Commission of Sichuan Province/ ; 24QNMP038//Health Commission of Sichuan Province Medical Science and Technology Program/ ; },
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology ; *Vagina/microbiology ; *Microbiota/physiology ; *Cervix Uteri/microbiology ; *Gastrointestinal Microbiome/physiology ; },
abstract = {BACKGROUND: An increasing number of studies indicate that the gut, cervical, and vaginal microbiota may play crucial roles in the development of cervical cancer (CC). However, the interactions between the microbiota and the host are yet unknown. To address this gap, a systematic review and meta-analysis were conducted to assess the microbiota alterations in a variety of body locations, including the gut and genital tract.
METHODS: Electronic searches of PubMed, Embase, Web of Science, and the Cochrane Library were conducted to retrieve eligible papers published from January 1, 2014, to January 1, 2024 (PROSPERO: CRD42024554433). This study was restricted to English-language studies reporting on alpha diversity, beta diversity, and relative abundance, as well as on patients with CC whose microbiota had been analyzed via next-generation sequencing technologies. To assess the risk of bias (RoB), we utilized the Newcastle‒Ottawa Quality Assessment Scale (NOS) and the ROBINS-I tool. For the meta-analysis, we employed Review Manager 5.4.
RESULTS: Thirty-six eligible studies were included in this review. The Chao1 index (SMD = 0.96, [95% CI: 0.71, 1.21], I[2] = 0%) and the Shannon index (SMD = 1.02, [95% CI: 0.53, 1.50], I[2] = 85%) values from vaginal samples were significantly greater in patients than in the controls. In the cervical samples, the Shannon index value (SMD = 1.29, [95% CI: 0.61, 1.97], I[2] = 93%) significantly increased, whereas the Chao1 index value did not significantly differ (SMD = 0.50, [95% CI: -0.46, 1.46], I[2] = 89%). The Shannon index value (SMD = 0.25, [95% CI: -0.22, 0.72], I[2] = 38%) did not significantly differ across the gut samples. The majority of studies (19/25) indicated that the patients and noncancer controls differed significantly in terms of beta diversity. Cancer-associated changes were observed, with a dramatic decrease in the Lactobacillus genus and significant increases in pathogenic bacteria, including the Anaerococcus, Peptostreptococcus, Porphyromonas, Prevotella, and Sneathia genera. Additionally, the impact of antineoplastic therapies on microbial diversity was inconsistently reported across several studies.
CONCLUSION: This systematic review elucidates the microbiota alterations associated with the prevalence of CC and its response to anti-tumor therapies, aiming to provide insights for future research directions and precision medicine strategies to enhance women's quality of life.
PROSPERO REGISTRATION: CRD42024554433.},
}
MeSH Terms:
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Humans
Female
*Uterine Cervical Neoplasms/microbiology
*Vagina/microbiology
*Microbiota/physiology
*Cervix Uteri/microbiology
*Gastrointestinal Microbiome/physiology
RevDate: 2025-02-15
CmpDate: 2025-02-15
A randomized controlled study protocol of the TOBBI trial: the effect of a 6 weeks intervention with synbiotics on the recovery speed of the gut microbiota after antibiotic treatment in Dutch toddlers.
BMC pediatrics, 25(1):117.
BACKGROUND: Antibiotic-induced disruption of the gut microbiome in the first 1000 days of life is linked to an increased risk of the development of immunological, metabolic, and neurobehavioral childhood-onset conditions. Supporting the recovery of the gut microbial community after it has been perturbed by antibiotics might be a promising strategy to reduce these risks. In this clinical study, the effect of a 6 weeks supplementation with synbiotics (Bifidobacterium breve M-16 V, short chain galacto-oligosaccharides and long chain fructo-oligosaccharides) after antibiotic treatment on the recovery speed of the gut microbiota of toddlers will be studied.
METHODS/DESIGN: A cohort of 126 Dutch toddlers aged 12 to 36 months old, who receive an amoxicillin or amoxicillin/clavulanic acid treatment, will be followed for 12 weeks. Participants will be randomized into an intervention group, who will consume the study product over a 6 weeks period starting at the last day of the antibiotic treatment or into a control group that will continue their usual eating pattern. Stool samples and their characteristics will be collected weekly by both groups. Stool samples will be analyzed for total microbiota and Bifidobacterium spp.. The differences in the proportion of Bifidobacterium out of total gut microbiota, composition of species belonging to Bifidobacterium, and beta diversity overtime will be compared between the two groups to study the effect of the intervention on the gut microbiota after perturbation. Furthermore, the effect of the treatment will also be studied in terms of the gut microbiota metabolic activity and stool characteristics. Additionally, food intake will be recorded to investigate whether diet, especially dietary fibers, may influence the gut microbiota as well. The findings may highlight a potential intervention strategy to support the recovery of the gut community after it has been perturbed by antibiotics in early life.
TRIAL REGISTRATION: The TOBBI trial was approved by the board of Medical Ethics Review Committee NedMec in June 2022 and registered at https://www.onderzoekmetmensen.nl/en/trial/20358 under the code NL75975.081.20, and at the World Health Organization at https://trialsearch.who.int/Trial2.aspx?TrialID=NL-OMON20358 under NTR-new: NL8996.
Additional Links: PMID-39955511
PubMed:
Citation:
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@article {pmid39955511,
year = {2025},
author = {Klomp, K and Alkema, M and Knol, J and Malinowska, AM and Belzer, C},
title = {A randomized controlled study protocol of the TOBBI trial: the effect of a 6 weeks intervention with synbiotics on the recovery speed of the gut microbiota after antibiotic treatment in Dutch toddlers.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {117},
pmid = {39955511},
issn = {1471-2431},
support = {AF18005//TKI agrifood/ ; AF18005//TKI agrifood/ ; AF18005//TKI agrifood/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant ; *Synbiotics/administration & dosage ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Child, Preschool ; Netherlands ; Amoxicillin/administration & dosage/therapeutic use ; Amoxicillin-Potassium Clavulanate Combination/therapeutic use ; Feces/microbiology ; Male ; Female ; Bifidobacterium breve ; },
abstract = {BACKGROUND: Antibiotic-induced disruption of the gut microbiome in the first 1000 days of life is linked to an increased risk of the development of immunological, metabolic, and neurobehavioral childhood-onset conditions. Supporting the recovery of the gut microbial community after it has been perturbed by antibiotics might be a promising strategy to reduce these risks. In this clinical study, the effect of a 6 weeks supplementation with synbiotics (Bifidobacterium breve M-16 V, short chain galacto-oligosaccharides and long chain fructo-oligosaccharides) after antibiotic treatment on the recovery speed of the gut microbiota of toddlers will be studied.
METHODS/DESIGN: A cohort of 126 Dutch toddlers aged 12 to 36 months old, who receive an amoxicillin or amoxicillin/clavulanic acid treatment, will be followed for 12 weeks. Participants will be randomized into an intervention group, who will consume the study product over a 6 weeks period starting at the last day of the antibiotic treatment or into a control group that will continue their usual eating pattern. Stool samples and their characteristics will be collected weekly by both groups. Stool samples will be analyzed for total microbiota and Bifidobacterium spp.. The differences in the proportion of Bifidobacterium out of total gut microbiota, composition of species belonging to Bifidobacterium, and beta diversity overtime will be compared between the two groups to study the effect of the intervention on the gut microbiota after perturbation. Furthermore, the effect of the treatment will also be studied in terms of the gut microbiota metabolic activity and stool characteristics. Additionally, food intake will be recorded to investigate whether diet, especially dietary fibers, may influence the gut microbiota as well. The findings may highlight a potential intervention strategy to support the recovery of the gut community after it has been perturbed by antibiotics in early life.
TRIAL REGISTRATION: The TOBBI trial was approved by the board of Medical Ethics Review Committee NedMec in June 2022 and registered at https://www.onderzoekmetmensen.nl/en/trial/20358 under the code NL75975.081.20, and at the World Health Organization at https://trialsearch.who.int/Trial2.aspx?TrialID=NL-OMON20358 under NTR-new: NL8996.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/drug effects
Infant
*Synbiotics/administration & dosage
*Anti-Bacterial Agents/therapeutic use/administration & dosage
Child, Preschool
Netherlands
Amoxicillin/administration & dosage/therapeutic use
Amoxicillin-Potassium Clavulanate Combination/therapeutic use
Feces/microbiology
Male
Female
Bifidobacterium breve
RevDate: 2025-02-15
CmpDate: 2025-02-15
Exploration of oral microbiota alteration and AI-driven non-invasive hyperspectral imaging for CAD prediction.
BMC cardiovascular disorders, 25(1):102.
BACKGROUND: Oral microbiome dysbiosis is an important risk factor affecting the occurrence and progression of coronary artery disease (CAD). However, the dysbiosis on the tongue in patients with CAD is still unclear, and whether the oral alteration caused by these disorders can be identified by other tools for CAD diagnosis needs to be further explored. Hyperspectral imaging (HSI) is characterized as high spectral resolution, broad spectral range, and superior spatial resolution. Hyperspectral images contain high-dimensional data that generally require machine learning algorithms for feature identification and model construction. Therefore, this study aims to investigate the variation of tongue microbiota and the effectiveness of HSI models in CAD diagnosis.
METHODS: Between 2023 and 2024, we prospectively approached 276 patients with chest pain and exhibiting risk for CAD who underwent coronary artery angiography (CAG). And 190 patients were enrolled in this study. Tongue dorsum swabs were collected for subsequent 16sRNA sequencing and microbiome analysis. Tongue dorsum features were extracted from hyperspectral images. The HSI analysis incorporated a total of 4750 hyperspectral images from all patients. All images are divided into training set (N = 2555), internal test set (N = 1095) and external test set (N = 1095). A total of 31 models were constructed. 30 single machine learning algorithms were used to construct and test the CAD prediction models. Furthermore, the best performing fusion model was established. The efficacy of the model was evaluated employing several metrics, including area under the curve (AUC), decision curve analysis (DCA), calibration curve, accuracy (ACC), sensitivity (SE), specificity (SP), positive predictive value (PPV), negative predictive value (NPV) and F1 score.
RESULTS: The 16sRNA sequencing results indicated significant dysbiosis in the oral microbiota of patients with CAD, with decreased microbial abundance, network complexity and stability. The fusion model (GP-GB-SVM) demonstrated the highest performance, achieving an AUC of 0.92, ACC of 0.82, SE of 0.70, SP of 0.92, PPV of 0.88 and NPV of 0.79 in the internal test set and AUC of 0.86, ACC of 0.70, SE of 0.90, SP of 0.46, PPV of 0.60 and NPV of 0.90 in the external test set.
CONCLUSION: These findings not only emphasize the significant alteration of microbiome colonized on the tongue dorsum in CAD patients but also demonstrate the tongue features associated with microbiome dysbiosis can be identified in hyperspectral images. Thereby the integration of HSI and machine learning provides novel insights into non-invasive diagnosis of CAD.
Additional Links: PMID-39955509
PubMed:
Citation:
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@article {pmid39955509,
year = {2025},
author = {Li, Z and Yang, X and Zhang, D and Shi, X and Lei, L and Zhou, F and Li, W and Xu, T and Liu, X and Wang, S and Yang, J and Wang, X and Zhong, Y and Yu, L},
title = {Exploration of oral microbiota alteration and AI-driven non-invasive hyperspectral imaging for CAD prediction.},
journal = {BMC cardiovascular disorders},
volume = {25},
number = {1},
pages = {102},
pmid = {39955509},
issn = {1471-2261},
support = {ICRCYG-2022-001//Cross-Innovation Talent Program of Renmin Hospital of Wuhan University/ ; 82270532//National Natural Science Foundation of China/ ; 2021CFA010//Foundation for Innovative Research Groups of Natural Science Foundation of Hubei Province/ ; 2042024kf0041//Central University Basic Research Fund of China/ ; },
mesh = {Humans ; Female ; Male ; *Tongue/microbiology/diagnostic imaging ; *Predictive Value of Tests ; *Coronary Artery Disease/diagnostic imaging/microbiology ; Middle Aged ; *Microbiota ; Prospective Studies ; Aged ; *Hyperspectral Imaging ; Dysbiosis/microbiology ; Machine Learning ; Bacteria/isolation & purification/genetics/classification ; Ribotyping ; Reproducibility of Results ; Coronary Angiography ; Risk Assessment ; Image Interpretation, Computer-Assisted ; },
abstract = {BACKGROUND: Oral microbiome dysbiosis is an important risk factor affecting the occurrence and progression of coronary artery disease (CAD). However, the dysbiosis on the tongue in patients with CAD is still unclear, and whether the oral alteration caused by these disorders can be identified by other tools for CAD diagnosis needs to be further explored. Hyperspectral imaging (HSI) is characterized as high spectral resolution, broad spectral range, and superior spatial resolution. Hyperspectral images contain high-dimensional data that generally require machine learning algorithms for feature identification and model construction. Therefore, this study aims to investigate the variation of tongue microbiota and the effectiveness of HSI models in CAD diagnosis.
METHODS: Between 2023 and 2024, we prospectively approached 276 patients with chest pain and exhibiting risk for CAD who underwent coronary artery angiography (CAG). And 190 patients were enrolled in this study. Tongue dorsum swabs were collected for subsequent 16sRNA sequencing and microbiome analysis. Tongue dorsum features were extracted from hyperspectral images. The HSI analysis incorporated a total of 4750 hyperspectral images from all patients. All images are divided into training set (N = 2555), internal test set (N = 1095) and external test set (N = 1095). A total of 31 models were constructed. 30 single machine learning algorithms were used to construct and test the CAD prediction models. Furthermore, the best performing fusion model was established. The efficacy of the model was evaluated employing several metrics, including area under the curve (AUC), decision curve analysis (DCA), calibration curve, accuracy (ACC), sensitivity (SE), specificity (SP), positive predictive value (PPV), negative predictive value (NPV) and F1 score.
RESULTS: The 16sRNA sequencing results indicated significant dysbiosis in the oral microbiota of patients with CAD, with decreased microbial abundance, network complexity and stability. The fusion model (GP-GB-SVM) demonstrated the highest performance, achieving an AUC of 0.92, ACC of 0.82, SE of 0.70, SP of 0.92, PPV of 0.88 and NPV of 0.79 in the internal test set and AUC of 0.86, ACC of 0.70, SE of 0.90, SP of 0.46, PPV of 0.60 and NPV of 0.90 in the external test set.
CONCLUSION: These findings not only emphasize the significant alteration of microbiome colonized on the tongue dorsum in CAD patients but also demonstrate the tongue features associated with microbiome dysbiosis can be identified in hyperspectral images. Thereby the integration of HSI and machine learning provides novel insights into non-invasive diagnosis of CAD.},
}
MeSH Terms:
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Humans
Female
Male
*Tongue/microbiology/diagnostic imaging
*Predictive Value of Tests
*Coronary Artery Disease/diagnostic imaging/microbiology
Middle Aged
*Microbiota
Prospective Studies
Aged
*Hyperspectral Imaging
Dysbiosis/microbiology
Machine Learning
Bacteria/isolation & purification/genetics/classification
Ribotyping
Reproducibility of Results
Coronary Angiography
Risk Assessment
Image Interpretation, Computer-Assisted
RevDate: 2025-02-15
CmpDate: 2025-02-15
Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.
BMC genomic data, 26(1):12.
OBJECTIVE: Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.
DATA DESCRIPTION: We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.
Additional Links: PMID-39955481
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@article {pmid39955481,
year = {2025},
author = {Wan, Y and Pike, R and Harley, A and Mumin, Z and Potterill, I and Meunier, D and Ganner, M and Getino, M and Coelho, J and Jauneikaite, E and Moganeradj, K and Brown, CS and Holmes, AH and Demirjian, A and Hopkins, KL and Pichon, B},
title = {Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {12},
pmid = {39955481},
issn = {2730-6844},
support = {PSN109/WT_/Wellcome Trust/United Kingdom ; NIHR200876//National Institute for Health and Care Research/ ; UGG10057//Price David Evans endowment/ ; },
mesh = {*Staphylococcus capitis/genetics/drug effects/isolation & purification ; *Microbial Sensitivity Tests ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Whole Genome Sequencing ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {OBJECTIVE: Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.
DATA DESCRIPTION: We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.},
}
MeSH Terms:
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hide MeSH Terms
*Staphylococcus capitis/genetics/drug effects/isolation & purification
*Microbial Sensitivity Tests
*Genome, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Humans
Whole Genome Sequencing
Staphylococcal Infections/microbiology/drug therapy
Drug Resistance, Multiple, Bacterial/genetics
RevDate: 2025-02-15
CmpDate: 2025-02-15
Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.
Scientific reports, 15(1):5619.
Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.
Additional Links: PMID-39955324
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@article {pmid39955324,
year = {2025},
author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO},
title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5619},
pmid = {39955324},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation & purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; },
abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/genetics
Male
Adult
*Athletes
Female
*Feces/microbiology
Metagenomics/methods
Prevotella/genetics/isolation & purification
Young Adult
Running
Faecalibacterium prausnitzii/genetics
RevDate: 2025-02-15
CmpDate: 2025-02-15
Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting.
Scientific reports, 15(1):5601.
There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analysed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Delivery method and antibiotic exposures during pregnancy and early childhood appeared to have limited effects on developmental trajectories of gut microbiota. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.
Additional Links: PMID-39955323
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@article {pmid39955323,
year = {2025},
author = {Seco-Hidalgo, V and Witney, AA and Chico, ME and Vaca, M and Arevalo, A and Schuyler, AJ and Platts-Mills, TAE and Ster, IC and Cooper, PJ},
title = {Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5601},
pmid = {39955323},
issn = {2045-2322},
support = {RO1-AI-20565/NH/NIH HHS/United States ; 088862/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; Child, Preschool ; *Rural Population ; Female ; *Poverty ; Male ; Ecuador ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; Pregnancy ; Infant, Newborn ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analysed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Delivery method and antibiotic exposures during pregnancy and early childhood appeared to have limited effects on developmental trajectories of gut microbiota. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.},
}
MeSH Terms:
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Humans
*Gastrointestinal Microbiome
Infant
Child, Preschool
*Rural Population
Female
*Poverty
Male
Ecuador
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
Longitudinal Studies
Pregnancy
Infant, Newborn
Bacteria/classification/genetics/isolation & purification
RevDate: 2025-02-15
Role of the microbiome in regulation of the immune system.
Allergology international : official journal of the Japanese Society of Allergology pii:S1323-8930(24)00163-1 [Epub ahead of print].
Immune health and metabolic functions are intimately connected via diet and the microbiota. Immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important mucosal and systemic ramifications. Microbial fermentation of dietary components in vivo generates thousands of molecules, some of which are integral components of the molecular circuitry that regulates immune and metabolic functions. These in turn protect against aberrant inflammatory or hyper-reactive processes and promote effector immune responses that quickly eliminate pathogens, such as SARS-CoV-2. Potent tolerance mechanisms should ensure that these immune cells do not over-react to non-pathogenic factors (e.g. food proteins), while maintaining the ability to respond to infectious challenges in a robust, effective and well controlled manner. In this review we examine the factors and mechanisms that shape microbiota composition and interactions with the host immune system, their associations with immune mediated disorders and strategies for intervention.
Additional Links: PMID-39955207
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PubMed:
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@article {pmid39955207,
year = {2025},
author = {Kim, S and Ndwandwe, C and Devotta, H and Kareem, L and Yao, L and O'Mahony, L},
title = {Role of the microbiome in regulation of the immune system.},
journal = {Allergology international : official journal of the Japanese Society of Allergology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alit.2024.12.006},
pmid = {39955207},
issn = {1440-1592},
abstract = {Immune health and metabolic functions are intimately connected via diet and the microbiota. Immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important mucosal and systemic ramifications. Microbial fermentation of dietary components in vivo generates thousands of molecules, some of which are integral components of the molecular circuitry that regulates immune and metabolic functions. These in turn protect against aberrant inflammatory or hyper-reactive processes and promote effector immune responses that quickly eliminate pathogens, such as SARS-CoV-2. Potent tolerance mechanisms should ensure that these immune cells do not over-react to non-pathogenic factors (e.g. food proteins), while maintaining the ability to respond to infectious challenges in a robust, effective and well controlled manner. In this review we examine the factors and mechanisms that shape microbiota composition and interactions with the host immune system, their associations with immune mediated disorders and strategies for intervention.},
}
RevDate: 2025-02-15
Methodological aspects of investigating the resistome in pig farm environments.
Journal of microbiological methods pii:S0167-7012(25)00019-3 [Epub ahead of print].
A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.
Additional Links: PMID-39954816
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PubMed:
Citation:
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@article {pmid39954816,
year = {2025},
author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nazirzadeh, L and Bongcam-Rudloff, E and Dicksved, J},
title = {Methodological aspects of investigating the resistome in pig farm environments.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107103},
doi = {10.1016/j.mimet.2025.107103},
pmid = {39954816},
issn = {1872-8359},
abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.},
}
RevDate: 2025-02-15
Neuro-nutraceuticals: Emerging molecular and functional insights into how natural products improve brain health.
The editors in assembling this Special Issue, "Neuro-nutraceuticals: Emerging Molecular and Functional Insights into how Natural Products Improve Brain Health", sought to advance our understanding of how such chemical entities alone or in group maintain brain metabolism and homeostasis so that neurons, glia and endothelial cells are healthy during development, ageing and in neuropathologies. The growth of interest in neuro-nutraceuticals and all aspects of their actions relevant to the health of the nervous system continues to amaze all. This Special Issue # 4 contains 39 articles, and we sought to highlight in this Special Issue important new advances and key issues pertinent to future clinical application of neuro-nutraceuticals. The diversity of topics covered is quite broad and includes significant articles on enteric microbiome and brain health. The Editors have tried to provide an up-to-date account of how nutraceuticals work at the molecular and cellular level, and what are the known molecular targets that ultimately can be leveraged clinically to enable the brain to function better. With respect to brain ailments and treatments, single molecule effects, and a therapeutic group of molecules from dietary herbals are discussed in this Special Issue.
Additional Links: PMID-39954790
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PubMed:
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@article {pmid39954790,
year = {2025},
author = {Mohanakumar, KP and Rendeiro, C and Beart, PM},
title = {Neuro-nutraceuticals: Emerging molecular and functional insights into how natural products improve brain health.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {105948},
doi = {10.1016/j.neuint.2025.105948},
pmid = {39954790},
issn = {1872-9754},
abstract = {The editors in assembling this Special Issue, "Neuro-nutraceuticals: Emerging Molecular and Functional Insights into how Natural Products Improve Brain Health", sought to advance our understanding of how such chemical entities alone or in group maintain brain metabolism and homeostasis so that neurons, glia and endothelial cells are healthy during development, ageing and in neuropathologies. The growth of interest in neuro-nutraceuticals and all aspects of their actions relevant to the health of the nervous system continues to amaze all. This Special Issue # 4 contains 39 articles, and we sought to highlight in this Special Issue important new advances and key issues pertinent to future clinical application of neuro-nutraceuticals. The diversity of topics covered is quite broad and includes significant articles on enteric microbiome and brain health. The Editors have tried to provide an up-to-date account of how nutraceuticals work at the molecular and cellular level, and what are the known molecular targets that ultimately can be leveraged clinically to enable the brain to function better. With respect to brain ailments and treatments, single molecule effects, and a therapeutic group of molecules from dietary herbals are discussed in this Special Issue.},
}
RevDate: 2025-02-15
High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.
International journal of food microbiology, 432:111098 pii:S0168-1605(25)00043-1 [Epub ahead of print].
The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.
Additional Links: PMID-39954350
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PubMed:
Citation:
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@article {pmid39954350,
year = {2025},
author = {Dong, Y and Liu, H and Habimana, O},
title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.},
journal = {International journal of food microbiology},
volume = {432},
number = {},
pages = {111098},
doi = {10.1016/j.ijfoodmicro.2025.111098},
pmid = {39954350},
issn = {1879-3460},
abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.},
}
RevDate: 2025-02-15
Advancements in pharmacological interventions for atopic dermatitis current strategies and future directions.
Inflammopharmacology [Epub ahead of print].
Atopic dermatitis (AD) is a complex chronic inflammatory skin disorder, with its incidence significantly increasing in recent years. The pathogenesis of AD is complex, involving multiple factors such as genetic susceptibility, dysbiosis of the skin microbiome, autoimmune abnormalities, impaired epidermal barrier function, and environmental factors. These factors collectively contribute to the high incidence of the disease and its significant socio-economic burden. This article reviews the pathogenesis of AD and analyzes the current traditional treatment approaches, including topical and systemic therapies, highlighting the issues they face. It focuses on the current status and treatment strategies. Specifically, as the significant heterogeneity of AD, treatment paradigms are gradually shifting from a "one-size-fits-all" approach to personalized treatments. The aim is to achieve more effective management of AD and address the issues arising from individual differences. Through these discussions, this article aims to provide new perspectives and strategies for the clinical treatment of AD, in order to reduce the disease burden on patients.
Additional Links: PMID-39954187
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Citation:
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@article {pmid39954187,
year = {2025},
author = {Zhang, Y and Yuan, S and Wu, Y and Nie, W and You, T and Yang, H and Liu, B},
title = {Advancements in pharmacological interventions for atopic dermatitis current strategies and future directions.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {39954187},
issn = {1568-5608},
support = {201805010006//Guangzhou key laboratory of construction and application of new drug screening model systems/ ; 2017KSYS002//Key Laboratory of New Drug Discovery and Evaluation of ordinary universities of Guangdong province/ ; Z155080000004//National Key Clinical Specialty Discipline Construction Program of China/ ; },
abstract = {Atopic dermatitis (AD) is a complex chronic inflammatory skin disorder, with its incidence significantly increasing in recent years. The pathogenesis of AD is complex, involving multiple factors such as genetic susceptibility, dysbiosis of the skin microbiome, autoimmune abnormalities, impaired epidermal barrier function, and environmental factors. These factors collectively contribute to the high incidence of the disease and its significant socio-economic burden. This article reviews the pathogenesis of AD and analyzes the current traditional treatment approaches, including topical and systemic therapies, highlighting the issues they face. It focuses on the current status and treatment strategies. Specifically, as the significant heterogeneity of AD, treatment paradigms are gradually shifting from a "one-size-fits-all" approach to personalized treatments. The aim is to achieve more effective management of AD and address the issues arising from individual differences. Through these discussions, this article aims to provide new perspectives and strategies for the clinical treatment of AD, in order to reduce the disease burden on patients.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Salivary microbiota characterization of Yerba Mate consumers in Uruguay.
Clinical oral investigations, 29(2):131.
INTRODUCTION: Yerba Mate (YM) is a green-colored infusion, derived from the Ilex paraguariensis plant, very popular and commonly consumed in Latin American countries (southern Brazil, Argentina, Paraguay, and Uruguay), rapidly gaining penetration in global markets, It's a beverage rich in polyphenols, alkaloids, and saponins, making its impact on the oral microbiome particularly interesting.
OBJECTIVES: This study aimed to characterize the composition of salivary microbiota in Uruguayan YM consumers and non-consumers, exploring potential implications for oral health.
MATERIALS AND METHODS: Salivary samples were collected from 24 YM consumers and 28 non-consumers in Uruguay (n = 52). Participants were dentistry students, aged 18 to 35, with no reported pathologies and who had no oral conditions after visual inspection. 16S rRNA gene metabarcoding Illumina sequencing was employed to analyze their microbial composition. Bioinformatic analysis was conducted to identify and compare microbial taxa between the two groups. Relevant demographic and dietary data were also collected and analyzed.
RESULTS: The salivary microbiome of YM consumers is not completely different from non-consumers, however, several particular characteristics were found in each group. Both YM consumers and non-consumers exhibited a high relative abundance of Streptococcus species, with Streptococcus oralis being more abundant in a subset of non-consumers suggesting that YM may help maintain a balanced oral microbiota. Although no significant differences were observed in the Shannon diversity index, YM consumers might have a more diverse microbiome than non-consumers (YM consumers showed significantly higher species richness (Chao1 index), a greater number of amplicon sequence variants (ASVs), and broader microbial diversity, as confirmed by multivariate analyses). While the presence of Prevotella spp. in YM consumers aligns with previous research on polyphenol-rich beverages, its role in oral health warrants further investigation.
CONCLUSIONS: This study highlights the influence of YM consumption on salivary microbiota composition and diversity. YM consumption was associated with increased microbial diversity and species richness, which may contribute to oral microbiome resilience and health. These findings underscore the impact of dietary habits on oral microbial communities and their potential implications for oral health management and disease prevention.
Additional Links: PMID-39954023
PubMed:
Citation:
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@article {pmid39954023,
year = {2025},
author = {Garcia, B and Dominguez, MF and Spangenberg, L and Fernandez-Calero, T},
title = {Salivary microbiota characterization of Yerba Mate consumers in Uruguay.},
journal = {Clinical oral investigations},
volume = {29},
number = {2},
pages = {131},
pmid = {39954023},
issn = {1436-3771},
support = {Alicuotas//Programa de Desarrollo de las Ciencias Básicas/ ; Alicuotas//Programa de Desarrollo de las Ciencias Básicas/ ; COF 03/11//FOCEM - Fondo para la Convergencia Estructural del Mercosur/ ; COF 03/11//FOCEM - Fondo para la Convergencia Estructural del Mercosur/ ; },
mesh = {Humans ; *Saliva/microbiology ; Uruguay ; *Microbiota ; Adult ; Female ; Male ; Adolescent ; *Ilex paraguariensis ; RNA, Ribosomal, 16S ; Beverages/microbiology ; },
abstract = {INTRODUCTION: Yerba Mate (YM) is a green-colored infusion, derived from the Ilex paraguariensis plant, very popular and commonly consumed in Latin American countries (southern Brazil, Argentina, Paraguay, and Uruguay), rapidly gaining penetration in global markets, It's a beverage rich in polyphenols, alkaloids, and saponins, making its impact on the oral microbiome particularly interesting.
OBJECTIVES: This study aimed to characterize the composition of salivary microbiota in Uruguayan YM consumers and non-consumers, exploring potential implications for oral health.
MATERIALS AND METHODS: Salivary samples were collected from 24 YM consumers and 28 non-consumers in Uruguay (n = 52). Participants were dentistry students, aged 18 to 35, with no reported pathologies and who had no oral conditions after visual inspection. 16S rRNA gene metabarcoding Illumina sequencing was employed to analyze their microbial composition. Bioinformatic analysis was conducted to identify and compare microbial taxa between the two groups. Relevant demographic and dietary data were also collected and analyzed.
RESULTS: The salivary microbiome of YM consumers is not completely different from non-consumers, however, several particular characteristics were found in each group. Both YM consumers and non-consumers exhibited a high relative abundance of Streptococcus species, with Streptococcus oralis being more abundant in a subset of non-consumers suggesting that YM may help maintain a balanced oral microbiota. Although no significant differences were observed in the Shannon diversity index, YM consumers might have a more diverse microbiome than non-consumers (YM consumers showed significantly higher species richness (Chao1 index), a greater number of amplicon sequence variants (ASVs), and broader microbial diversity, as confirmed by multivariate analyses). While the presence of Prevotella spp. in YM consumers aligns with previous research on polyphenol-rich beverages, its role in oral health warrants further investigation.
CONCLUSIONS: This study highlights the influence of YM consumption on salivary microbiota composition and diversity. YM consumption was associated with increased microbial diversity and species richness, which may contribute to oral microbiome resilience and health. These findings underscore the impact of dietary habits on oral microbial communities and their potential implications for oral health management and disease prevention.},
}
MeSH Terms:
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Humans
*Saliva/microbiology
Uruguay
*Microbiota
Adult
Female
Male
Adolescent
*Ilex paraguariensis
RNA, Ribosomal, 16S
Beverages/microbiology
RevDate: 2025-02-15
Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.
Animal microbiome, 7(1):15.
Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.
Additional Links: PMID-39955557
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@article {pmid39955557,
year = {2025},
author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A},
title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {15},
pmid = {39955557},
issn = {2524-4671},
support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.},
}
RevDate: 2025-02-15
Corrigendum to "Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages" [964 (2025) 178524].
Additional Links: PMID-39955156
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PubMed:
Citation:
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@article {pmid39955156,
year = {2025},
author = {Xu, M and Liu, X and Chen, T and Zhao, Y and Ma, L and Shi, X and Chen, X and Shi, Y and Adams, JM},
title = {Corrigendum to "Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages" [964 (2025) 178524].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {178834},
doi = {10.1016/j.scitotenv.2025.178834},
pmid = {39955156},
issn = {1879-1026},
}
RevDate: 2025-02-15
Application of photosensitive microalgae in targeted tumor therapy.
Advanced drug delivery reviews pii:S0169-409X(25)00004-3 [Epub ahead of print].
Microalgae present a novel and multifaceted approach to cancer therapy by modulating the tumor-associated microbiome (TAM) and the tumor microenvironment (TME). Through their ability to restore gut microbiota balance, reduce inflammation, and enhance immune responses, microalgae contribute to improved cancer treatment outcomes. As photosynthetic microorganisms, microalgae exhibit inherent anti-tumor, antioxidant, and immune-regulating properties, making them valuable in photodynamic therapy (PDT) and tumor imaging due to their capacity to generate reactive oxygen species (ROS). Additionally, microalgae serve as effective drug delivery vehicles, leveraging their biocompatibility and unique structural properties to target the TME more precisely. Microalgae-based microrobots further expand their therapeutic potential by autonomously navigating complex biological environments, offering a promising future for precision-targeted cancer treatments. We position microalgae as a multifunctional agent capable of modulating TAM, offering novel strategies to enhance TME and improve the efficacy of cancer therapies.
Additional Links: PMID-39955076
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Citation:
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@article {pmid39955076,
year = {2025},
author = {Wang, R and Wang, Z and Zhang, M and Zhong, D and Zhou, M},
title = {Application of photosensitive microalgae in targeted tumor therapy.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115519},
doi = {10.1016/j.addr.2025.115519},
pmid = {39955076},
issn = {1872-8294},
abstract = {Microalgae present a novel and multifaceted approach to cancer therapy by modulating the tumor-associated microbiome (TAM) and the tumor microenvironment (TME). Through their ability to restore gut microbiota balance, reduce inflammation, and enhance immune responses, microalgae contribute to improved cancer treatment outcomes. As photosynthetic microorganisms, microalgae exhibit inherent anti-tumor, antioxidant, and immune-regulating properties, making them valuable in photodynamic therapy (PDT) and tumor imaging due to their capacity to generate reactive oxygen species (ROS). Additionally, microalgae serve as effective drug delivery vehicles, leveraging their biocompatibility and unique structural properties to target the TME more precisely. Microalgae-based microrobots further expand their therapeutic potential by autonomously navigating complex biological environments, offering a promising future for precision-targeted cancer treatments. We position microalgae as a multifunctional agent capable of modulating TAM, offering novel strategies to enhance TME and improve the efficacy of cancer therapies.},
}
RevDate: 2025-02-15
Impact of Streptozotocin-Induced Type 1 and Type 2 Diabetes on Ocular Surface Microbial Signatures in C57BL/6J Mice.
Experimental eye research pii:S0014-4835(25)00053-3 [Epub ahead of print].
The ocular surface (OS), like other mucosal sites, hosts a diverse microbiome. However, the impact of hyperglycemia associated with diabetes on OS microbial composition remains poorly understood. In this study, we established type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM) models in C57BL/6J mice by administering high-dose streptozotocin (STZ) for T1DM and low-dose STZ combined with a high-fat diet for T2DM. The OS microbiome was characterized and analyzed using 16S rRNA sequencing. The results showed that neither T1DM nor T2DM significantly affected microbial richness compared to normal mice; however, T2DM led to a significant reduction in microbial diversity. This reduction in microbial diversity in T2DM is consistent with known microbial dysbiosis in diabetes, which may contribute to the pathogenesis of ocular complications such as dry eye disease and diabetic retinopathy. Community composition analysis identified Proteobacteria, Pelagibacterium, and Aliihoeflea as the core OS bacteria in normal mice. Diabetes significantly altered the OS microbial composition at various taxonomic levels. Specifically, T1DM was associated with 9 signature bacterial species, including Oceanospirillales, Bacillales, Halomonas, unclassified_f_Lachnospiraceae, and Anoxybacillus. T2DM exhibited 17 bacterial markers, including Firmicutes, Staphylococcus, Corynebacterium, and Parasutterella. Functional prediction of the microbiota using PICRUSt2 indicated potential impairments in carbohydrate metabolism due to diabetes. In conclusion, diabetic mice exhibit severe dysregulation of their OS microbiota, and restoring microbial balance in diabetic patients may represent a promising strategy for preventing and treating diabetic OS pathologies.
Additional Links: PMID-39955022
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PubMed:
Citation:
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@article {pmid39955022,
year = {2025},
author = {Jiao, X and Li, Z},
title = {Impact of Streptozotocin-Induced Type 1 and Type 2 Diabetes on Ocular Surface Microbial Signatures in C57BL/6J Mice.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {110282},
doi = {10.1016/j.exer.2025.110282},
pmid = {39955022},
issn = {1096-0007},
abstract = {The ocular surface (OS), like other mucosal sites, hosts a diverse microbiome. However, the impact of hyperglycemia associated with diabetes on OS microbial composition remains poorly understood. In this study, we established type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM) models in C57BL/6J mice by administering high-dose streptozotocin (STZ) for T1DM and low-dose STZ combined with a high-fat diet for T2DM. The OS microbiome was characterized and analyzed using 16S rRNA sequencing. The results showed that neither T1DM nor T2DM significantly affected microbial richness compared to normal mice; however, T2DM led to a significant reduction in microbial diversity. This reduction in microbial diversity in T2DM is consistent with known microbial dysbiosis in diabetes, which may contribute to the pathogenesis of ocular complications such as dry eye disease and diabetic retinopathy. Community composition analysis identified Proteobacteria, Pelagibacterium, and Aliihoeflea as the core OS bacteria in normal mice. Diabetes significantly altered the OS microbial composition at various taxonomic levels. Specifically, T1DM was associated with 9 signature bacterial species, including Oceanospirillales, Bacillales, Halomonas, unclassified_f_Lachnospiraceae, and Anoxybacillus. T2DM exhibited 17 bacterial markers, including Firmicutes, Staphylococcus, Corynebacterium, and Parasutterella. Functional prediction of the microbiota using PICRUSt2 indicated potential impairments in carbohydrate metabolism due to diabetes. In conclusion, diabetic mice exhibit severe dysregulation of their OS microbiota, and restoring microbial balance in diabetic patients may represent a promising strategy for preventing and treating diabetic OS pathologies.},
}
RevDate: 2025-02-15
Malignant Tumors in Vagal-innervated Organs: Exploring Its Homeostatic Role.
Cancer letters pii:S0304-3835(25)00103-X [Epub ahead of print].
Cancer remains a significant global health challenge, with its progression shaped by complex and multifactorial mechanisms. Recent research suggests that the vagus nerve could play a critical role in mediating communication between the tumor microenvironment and the central nervous system (CNS). This review highlights the diversity of vagal afferent receptors, which could position the vagus nerve as a unique pathway for transmitting immune, metabolic, mechanical, and chemical signals from tumors to the CNS. Such signaling could influence systemic disease progression and tumor-related responses. Additionally, the vagus nerve's interactions with the microbiome and the renin-angiotensin system (RAS)-both implicated in cancer biology-further underscore its potential central role in modulating tumor-related processes. Contradictions in the literature, particularly concerning vagal fibers, illustrate the complexity of its involvement in tumor progression, with both tumor-promoting and tumor-suppressive effects reported depending on cancer type and context. These contradictions often overlook certain experimental biases, such as the failure to distinguish between vagal afferent and efferent fibers during vagotomies or the localized parasympathetic effects that cannot always be extrapolated to the systemic level. By focusing on the homeostatic role of the vagus nerve, understanding these mechanisms could open the door to new perspectives in cancer research related to the vagus nerve and lead to potential therapeutic innovations.
Additional Links: PMID-39954934
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@article {pmid39954934,
year = {2025},
author = {Martinez, P and Sabatier, JM},
title = {Malignant Tumors in Vagal-innervated Organs: Exploring Its Homeostatic Role.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217539},
doi = {10.1016/j.canlet.2025.217539},
pmid = {39954934},
issn = {1872-7980},
abstract = {Cancer remains a significant global health challenge, with its progression shaped by complex and multifactorial mechanisms. Recent research suggests that the vagus nerve could play a critical role in mediating communication between the tumor microenvironment and the central nervous system (CNS). This review highlights the diversity of vagal afferent receptors, which could position the vagus nerve as a unique pathway for transmitting immune, metabolic, mechanical, and chemical signals from tumors to the CNS. Such signaling could influence systemic disease progression and tumor-related responses. Additionally, the vagus nerve's interactions with the microbiome and the renin-angiotensin system (RAS)-both implicated in cancer biology-further underscore its potential central role in modulating tumor-related processes. Contradictions in the literature, particularly concerning vagal fibers, illustrate the complexity of its involvement in tumor progression, with both tumor-promoting and tumor-suppressive effects reported depending on cancer type and context. These contradictions often overlook certain experimental biases, such as the failure to distinguish between vagal afferent and efferent fibers during vagotomies or the localized parasympathetic effects that cannot always be extrapolated to the systemic level. By focusing on the homeostatic role of the vagus nerve, understanding these mechanisms could open the door to new perspectives in cancer research related to the vagus nerve and lead to potential therapeutic innovations.},
}
RevDate: 2025-02-15
Suppression of Alzheimer's disease by Agaricus sinodeliciosus var. Chaidam exopolysaccharide with amyloid-β clearance activity via gut microbiota-metabolite regulation.
International journal of biological macromolecules pii:S0141-8130(25)01597-1 [Epub ahead of print].
Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease (AD), characterized by cognitive impairment, and there remains a lack of effective functional compound with Aβ clearance activity. To elucidate the effect of exopolysaccharide (EPS) extracted from Agaricus sinodeliciosus var. Chaidam on Aβ1-42- induced AD rat and uncover the underlying mechanism, the neuroprotective activity of EPS was evaluated using immunofluorescence, immunohistochemistry, western blot, RT-qPCR, microbiomics and metabolomics. The results demonstrated that EPS exhibited significant anti-AD efficacy, as evidenced by improved cognitive function and spatial memory, balanced brain redox status, suppressed neuroinflammatory responses. EPS substantially reduced Aβ1-42 accumulation in the hippocampus by activating Aβ-phagocytic microglia through the mTOR-HIF-1α pathway. Importantly, EPS reconstructed gut microbiota composition by increasing the relative abundance of Ruminococcaceae and reduced Erysipelotrichaceae. The reshaped gut microbiome and the formation of the metabolite serotonin were associated with behavioral alterations, neuroinflammation, and brain oxidative status. Thus, EPS significantly alleviated cognitive deficit and neuroinflammation in Aβ1-42-induced AD rats, potentially by enhancing microglial phagocytosis of Aβ1-42 and modulating the gut microbiome and serotonin production. Collectively, EPS from A. sinodeliciosus var. Chaidam polysaccharide may serve as a novel Aβ1-42-targeted approach for anti-AD therapy.
Additional Links: PMID-39954909
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@article {pmid39954909,
year = {2025},
author = {Lu, H and Liu, S and Zhang, S and Chen, J and Chen, Q},
title = {Suppression of Alzheimer's disease by Agaricus sinodeliciosus var. Chaidam exopolysaccharide with amyloid-β clearance activity via gut microbiota-metabolite regulation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141048},
doi = {10.1016/j.ijbiomac.2025.141048},
pmid = {39954909},
issn = {1879-0003},
abstract = {Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease (AD), characterized by cognitive impairment, and there remains a lack of effective functional compound with Aβ clearance activity. To elucidate the effect of exopolysaccharide (EPS) extracted from Agaricus sinodeliciosus var. Chaidam on Aβ1-42- induced AD rat and uncover the underlying mechanism, the neuroprotective activity of EPS was evaluated using immunofluorescence, immunohistochemistry, western blot, RT-qPCR, microbiomics and metabolomics. The results demonstrated that EPS exhibited significant anti-AD efficacy, as evidenced by improved cognitive function and spatial memory, balanced brain redox status, suppressed neuroinflammatory responses. EPS substantially reduced Aβ1-42 accumulation in the hippocampus by activating Aβ-phagocytic microglia through the mTOR-HIF-1α pathway. Importantly, EPS reconstructed gut microbiota composition by increasing the relative abundance of Ruminococcaceae and reduced Erysipelotrichaceae. The reshaped gut microbiome and the formation of the metabolite serotonin were associated with behavioral alterations, neuroinflammation, and brain oxidative status. Thus, EPS significantly alleviated cognitive deficit and neuroinflammation in Aβ1-42-induced AD rats, potentially by enhancing microglial phagocytosis of Aβ1-42 and modulating the gut microbiome and serotonin production. Collectively, EPS from A. sinodeliciosus var. Chaidam polysaccharide may serve as a novel Aβ1-42-targeted approach for anti-AD therapy.},
}
RevDate: 2025-02-15
Rotavirus regulates the gut microhabitat immune response through the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to lactose intolerance.
International immunopharmacology, 150:114275 pii:S1567-5769(25)00265-6 [Epub ahead of print].
Lactose intolerance (LI) is a significant contributor to diarrhea in infants and young children. Recent studies suggest a potential link between rotavirus (RV) infection and alterations in gut microbiota, which may play a role in the mechanism of LI. However, the precise underlying mechanism remains unclear and requires urgent clarification. In this study, we combined insights from immunology and gut microbiome research to propose that the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway, triggered by gut microbiota, may be involved. To investigate this, we established a LI animal model using 7-day-old BALB/c mice, which were infected with RV via oral gavage. The syndromes of mice were carefully recorded and compared during the intervention experiment. Notably, we measured the the expression levels of immunocytokines and phosphorylated signaling proteins, including IL-22, phosphorylated STAT3, and RegIIIγ. Additionally, we assessed the relationships between gut microbiota and these key elements. Our results indicated that RV indeed causes LI, as severe diarrhea was observed in the mice during the first three days of RV infection, subsiding after seven days. ELISA results revealed an increase in IL-22 levels, phosphorylated STAT3, and RegIIIγ, suggesting that the mechanism of LI associated with RV is linked to the classical IL-22/pSTAT3/RegIIIγ signaling pathway. Furthermore, our analysis of the connections between gut microbes and this signaling pathway indicated that "Bacteroidetes" and Firmicutes were significantly positively correlated with IL-22 and lactase, respectively. This finding implies that alterations in gut microbiota may serve as a potential switch for the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to increased lactase levels. In summary, our study demonstrated that the development of LI is associated with the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway alongside changes in gut microbes during RV infection. This provides valuable insights into the mechanisms underlying LI and its clinical treatment through moduLation of the gut microbiome.
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PubMed:
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@article {pmid39954663,
year = {2025},
author = {Shen, J and Xiao, Y and Bi, H and Guo, R and Qu, M and Ding, R and Zhang, X and Li, H and Han, M and Huang, S},
title = {Rotavirus regulates the gut microhabitat immune response through the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to lactose intolerance.},
journal = {International immunopharmacology},
volume = {150},
number = {},
pages = {114275},
doi = {10.1016/j.intimp.2025.114275},
pmid = {39954663},
issn = {1878-1705},
abstract = {Lactose intolerance (LI) is a significant contributor to diarrhea in infants and young children. Recent studies suggest a potential link between rotavirus (RV) infection and alterations in gut microbiota, which may play a role in the mechanism of LI. However, the precise underlying mechanism remains unclear and requires urgent clarification. In this study, we combined insights from immunology and gut microbiome research to propose that the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway, triggered by gut microbiota, may be involved. To investigate this, we established a LI animal model using 7-day-old BALB/c mice, which were infected with RV via oral gavage. The syndromes of mice were carefully recorded and compared during the intervention experiment. Notably, we measured the the expression levels of immunocytokines and phosphorylated signaling proteins, including IL-22, phosphorylated STAT3, and RegIIIγ. Additionally, we assessed the relationships between gut microbiota and these key elements. Our results indicated that RV indeed causes LI, as severe diarrhea was observed in the mice during the first three days of RV infection, subsiding after seven days. ELISA results revealed an increase in IL-22 levels, phosphorylated STAT3, and RegIIIγ, suggesting that the mechanism of LI associated with RV is linked to the classical IL-22/pSTAT3/RegIIIγ signaling pathway. Furthermore, our analysis of the connections between gut microbes and this signaling pathway indicated that "Bacteroidetes" and Firmicutes were significantly positively correlated with IL-22 and lactase, respectively. This finding implies that alterations in gut microbiota may serve as a potential switch for the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to increased lactase levels. In summary, our study demonstrated that the development of LI is associated with the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway alongside changes in gut microbes during RV infection. This provides valuable insights into the mechanisms underlying LI and its clinical treatment through moduLation of the gut microbiome.},
}
RevDate: 2025-02-15
Ectomycorrhizal fungi and biochar promote soil recalcitrant carbon increases under arsenic stress.
Journal of hazardous materials, 489:137598 pii:S0304-3894(25)00512-6 [Epub ahead of print].
Globally, vast mining areas (∼31,396.3 km[2]) hold significant potential for soil carbon sequestration. However, the sequestration capacity of mine soils is closely linked to contamination characteristics and restoration strategies. Arsenic, a highly toxic metalloid prevalent in acid mine soils, affects carbon turnover through its interactions with soil compounds. Nevertheless, the underlying mechanisms remain inadequately understood. This study introduces a phytobial remediation approach combining ectomycorrhizal fungus (Suillus luteus) inoculated into Pinus massoniana and biochar as a soil amendment. Results demonstrated that S. luteus extended apoplastic spaces to absorb arsenic into root cell intervals while encapsulating organic matter into aggregates. Biochar further promoted recalcitrant carbon formation, significantly increasing aggregate-carbon, particulate organic carbon (POC), and mineral-associated organic carbon (MAOC) by 3.15-, 1.74-, and 2.33-fold, respectively, compared to controls. Distinct hyphosphere microbiomes were observed in the combined treatment (BS), with enhanced microbial diversity, enzyme activity, carbon-sequestration genes, and necromass production, indicating the pivotal role of soil microorganisms in stable carbon pool formation. These synergistic effects not only facilitated arsenic detoxification but also significantly contributed to carbon stabilization.
Additional Links: PMID-39954432
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@article {pmid39954432,
year = {2025},
author = {Zhang, X and Liu, Y and Mo, X and Huang, Z and Zhu, Y and Li, H and Jiang, L and Tan, Z and Yang, Z and Zhu, Y and Huang, J and Zeng, B and Zhuo, R},
title = {Ectomycorrhizal fungi and biochar promote soil recalcitrant carbon increases under arsenic stress.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137598},
doi = {10.1016/j.jhazmat.2025.137598},
pmid = {39954432},
issn = {1873-3336},
abstract = {Globally, vast mining areas (∼31,396.3 km[2]) hold significant potential for soil carbon sequestration. However, the sequestration capacity of mine soils is closely linked to contamination characteristics and restoration strategies. Arsenic, a highly toxic metalloid prevalent in acid mine soils, affects carbon turnover through its interactions with soil compounds. Nevertheless, the underlying mechanisms remain inadequately understood. This study introduces a phytobial remediation approach combining ectomycorrhizal fungus (Suillus luteus) inoculated into Pinus massoniana and biochar as a soil amendment. Results demonstrated that S. luteus extended apoplastic spaces to absorb arsenic into root cell intervals while encapsulating organic matter into aggregates. Biochar further promoted recalcitrant carbon formation, significantly increasing aggregate-carbon, particulate organic carbon (POC), and mineral-associated organic carbon (MAOC) by 3.15-, 1.74-, and 2.33-fold, respectively, compared to controls. Distinct hyphosphere microbiomes were observed in the combined treatment (BS), with enhanced microbial diversity, enzyme activity, carbon-sequestration genes, and necromass production, indicating the pivotal role of soil microorganisms in stable carbon pool formation. These synergistic effects not only facilitated arsenic detoxification but also significantly contributed to carbon stabilization.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Crosstalk Between the Skin Environment and Microbial Community in Immune-Related Skin Diseases.
Clinical reviews in allergy & immunology, 68(1):16.
The skin surface hosts diverse skin microbiota, including bacteria, fungi, and viruses. Intricate interactions between the skin microenvironment and microbial community are crucial for maintaining cutaneous homeostasis. This review explores the bidirectional relationship between the skin ecosystem and its microbiota. The skin microenvironment is shaped by a combination of intrinsic factors, dominated by sweat glands and pilosebaceous units, and external factors, such as UV radiation and personal care products, which create distinct niches that influence microbial colonization patterns across different skin regions. The skin microbiome, in turn, modulates the physical, chemical, immunological, and microbial barriers of the skin. We also discuss the alterations in this crosstalk in various immune-related skin conditions such as atopic dermatitis, psoriasis, rosacea, hidradenitis suppurativa, skin cancer, and aging. Understanding these interactions is vital for developing targeted microbiome-based therapies for various skin disorders. Further researches are needed to deepen insights into the microbial roles and their therapeutic potentials in skin health and disease.
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@article {pmid39954089,
year = {2025},
author = {Liu, K and Deng, S and Zhou, Y and Xu, B and Zhang, Y and Li, W and Liu, X and Yao, X},
title = {Crosstalk Between the Skin Environment and Microbial Community in Immune-Related Skin Diseases.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {16},
pmid = {39954089},
issn = {1559-0267},
support = {82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology ; *Skin Diseases/immunology/etiology/microbiology ; Animals ; Disease Susceptibility ; Cellular Microenvironment/immunology ; },
abstract = {The skin surface hosts diverse skin microbiota, including bacteria, fungi, and viruses. Intricate interactions between the skin microenvironment and microbial community are crucial for maintaining cutaneous homeostasis. This review explores the bidirectional relationship between the skin ecosystem and its microbiota. The skin microenvironment is shaped by a combination of intrinsic factors, dominated by sweat glands and pilosebaceous units, and external factors, such as UV radiation and personal care products, which create distinct niches that influence microbial colonization patterns across different skin regions. The skin microbiome, in turn, modulates the physical, chemical, immunological, and microbial barriers of the skin. We also discuss the alterations in this crosstalk in various immune-related skin conditions such as atopic dermatitis, psoriasis, rosacea, hidradenitis suppurativa, skin cancer, and aging. Understanding these interactions is vital for developing targeted microbiome-based therapies for various skin disorders. Further researches are needed to deepen insights into the microbial roles and their therapeutic potentials in skin health and disease.},
}
MeSH Terms:
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Humans
*Microbiota/immunology
*Skin/microbiology/immunology
*Skin Diseases/immunology/etiology/microbiology
Animals
Disease Susceptibility
Cellular Microenvironment/immunology
RevDate: 2025-02-15
Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.
Molecular ecology [Epub ahead of print].
Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.
Additional Links: PMID-39953749
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PubMed:
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@article {pmid39953749,
year = {2025},
author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A},
title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17695},
doi = {10.1111/mec.17695},
pmid = {39953749},
issn = {1365-294X},
support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.},
}
RevDate: 2025-02-15
Genetic risk variants implicate impaired maintenance and repair of periodontal tissues as causal for periodontitis-A synthesis of recent findings.
Periodontology 2000 [Epub ahead of print].
Periodontitis is a complex inflammatory disease in which the host genome, in conjunction with extrinsic factors, determines susceptibility and progression. Genetic predisposition is the strongest risk factor in the first decades of life. As people age, chronic exposure to the periodontal microbiome puts a strain on the proper maintenance of barrier function. This review summarizes our current knowledge on genetic risk factors implicated in periodontitis, derived (i) from hypothesis-free systematic whole genome-profiling studies (genome-wide association studies [GWAS] and quantitative trait loci [QTL] mapping studies), and independently validated through further unbiased approaches; (ii) from monogenic and oligogenic forms of periodontitis; and (iii) from syndromic forms of periodontitis. The genes include, but are not limited to, SIGLEC5, PLG, ROBO2, ABCA1, PF4, and CTSC. Notably, CTSC and PLG gene mutations were also identified in non-syndromic and syndromic forms of prepubertal and early-onset periodontitis. The functions of the identified genes in this review suggest that the pathways affected by the periodontitis-associated gene variants converge in functions involved in the maintenance and repair of structural integrity of the periodontal tissues. Particularly, these genes play a role in the healing of inflamed and ulcerated periodontal tissues, including roles in fibrinolysis, extrusion of cellular debris, extracellular matrix remodeling and angiogenesis. Syndromes that include periodontitis in their phenotype indicate that neutrophils play an important role in the regulation of inflammation in the periodontium. The established genetic susceptibility genes therefore collectively provide new insights into the molecular mechanisms and plausible causal factors underlying periodontitis.
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@article {pmid39953674,
year = {2025},
author = {Schaefer, AS and Nibali, L and Zoheir, N and Moutsopoulos, NM and Loos, BG},
title = {Genetic risk variants implicate impaired maintenance and repair of periodontal tissues as causal for periodontitis-A synthesis of recent findings.},
journal = {Periodontology 2000},
volume = {},
number = {},
pages = {},
doi = {10.1111/prd.12622},
pmid = {39953674},
issn = {1600-0757},
support = {//NIH/ ; },
abstract = {Periodontitis is a complex inflammatory disease in which the host genome, in conjunction with extrinsic factors, determines susceptibility and progression. Genetic predisposition is the strongest risk factor in the first decades of life. As people age, chronic exposure to the periodontal microbiome puts a strain on the proper maintenance of barrier function. This review summarizes our current knowledge on genetic risk factors implicated in periodontitis, derived (i) from hypothesis-free systematic whole genome-profiling studies (genome-wide association studies [GWAS] and quantitative trait loci [QTL] mapping studies), and independently validated through further unbiased approaches; (ii) from monogenic and oligogenic forms of periodontitis; and (iii) from syndromic forms of periodontitis. The genes include, but are not limited to, SIGLEC5, PLG, ROBO2, ABCA1, PF4, and CTSC. Notably, CTSC and PLG gene mutations were also identified in non-syndromic and syndromic forms of prepubertal and early-onset periodontitis. The functions of the identified genes in this review suggest that the pathways affected by the periodontitis-associated gene variants converge in functions involved in the maintenance and repair of structural integrity of the periodontal tissues. Particularly, these genes play a role in the healing of inflamed and ulcerated periodontal tissues, including roles in fibrinolysis, extrusion of cellular debris, extracellular matrix remodeling and angiogenesis. Syndromes that include periodontitis in their phenotype indicate that neutrophils play an important role in the regulation of inflammation in the periodontium. The established genetic susceptibility genes therefore collectively provide new insights into the molecular mechanisms and plausible causal factors underlying periodontitis.},
}
RevDate: 2025-02-15
Microbial Dysbiosis, Titanium Release, and Peri-implantitis.
Journal of dental research [Epub ahead of print].
The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.
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PubMed:
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@article {pmid39953673,
year = {2025},
author = {Kotsakis, GA and Ganesan, SM},
title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241307939},
doi = {10.1177/00220345241307939},
pmid = {39953673},
issn = {1544-0591},
abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.
Journal of translational medicine, 23(1):186.
Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.
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@article {pmid39953591,
year = {2025},
author = {Chen, H and Yao, X and Yang, C and Zhang, Y and Dong, H and Zhai, J and Fan, D and Zhou, Q},
title = {Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {186},
pmid = {39953591},
issn = {1479-5876},
support = {YCZYPT [2018]06//National Human Genetic Resource Sharing Service Platform/ ; },
mesh = {Humans ; *Lung Neoplasms/blood/microbiology/genetics ; *Metagenomics/methods ; *Biomarkers, Tumor/blood ; Female ; Male ; Middle Aged ; Metagenome/genetics ; Aged ; Case-Control Studies ; ROC Curve ; },
abstract = {Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.},
}
MeSH Terms:
show MeSH Terms
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Humans
*Lung Neoplasms/blood/microbiology/genetics
*Metagenomics/methods
*Biomarkers, Tumor/blood
Female
Male
Middle Aged
Metagenome/genetics
Aged
Case-Control Studies
ROC Curve
RevDate: 2025-02-14
Child and Adult Seborrheic Dermatitis: A Narrative Review of the Current Treatment Landscape.
Dermatology and therapy [Epub ahead of print].
INTRODUCTION: Seborrheic dermatitis (SD) is a common, chronic inflammatory skin condition affecting sebaceous gland-rich areas of the skin. The multifactorial etiology of SD involves sebocyte activity, skin microbiome dysbiosis, and immune factors. Various treatment options exist for management of SD.
METHODS: A PubMed search conducted on November 1, 2024 using the terms "seborrheic dermatitis" and "treatment" (restricted to 2019-2024) yielded 389 results, from which relevant papers and additional references were included in this review.
DISCUSSION: Topical antifungals, topical corticosteroids, and topical calcineurin inhibitors are first-line treatments for SD; however, long-term use of each of these may be limited by varying side effects. Roflumilast foam is a newly approved topical with potential to become a first-line treatment. Myriad systemic treatments exist as second- and third-line treatments for cases of moderate-to-severe and/or recalcitrant SD. Procedural interventions of varying efficacy exist.
CONCLUSIONS: The treatment of SD requires an individualized approach, utilizing a range of topical, systemic, and procedural interventions. The advent of new treatments like roflumilast foam offers novel, well-tolerated, and safer options than what has been available in the past.
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@article {pmid39953371,
year = {2025},
author = {Vidal, SI and Menta, N and Green, L},
title = {Child and Adult Seborrheic Dermatitis: A Narrative Review of the Current Treatment Landscape.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {39953371},
issn = {2193-8210},
abstract = {INTRODUCTION: Seborrheic dermatitis (SD) is a common, chronic inflammatory skin condition affecting sebaceous gland-rich areas of the skin. The multifactorial etiology of SD involves sebocyte activity, skin microbiome dysbiosis, and immune factors. Various treatment options exist for management of SD.
METHODS: A PubMed search conducted on November 1, 2024 using the terms "seborrheic dermatitis" and "treatment" (restricted to 2019-2024) yielded 389 results, from which relevant papers and additional references were included in this review.
DISCUSSION: Topical antifungals, topical corticosteroids, and topical calcineurin inhibitors are first-line treatments for SD; however, long-term use of each of these may be limited by varying side effects. Roflumilast foam is a newly approved topical with potential to become a first-line treatment. Myriad systemic treatments exist as second- and third-line treatments for cases of moderate-to-severe and/or recalcitrant SD. Procedural interventions of varying efficacy exist.
CONCLUSIONS: The treatment of SD requires an individualized approach, utilizing a range of topical, systemic, and procedural interventions. The advent of new treatments like roflumilast foam offers novel, well-tolerated, and safer options than what has been available in the past.},
}
RevDate: 2025-02-14
The researchers on a quest to protect the gut from antibiotics.
Additional Links: PMID-39953156
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@article {pmid39953156,
year = {2025},
author = {Dolgin, E},
title = {The researchers on a quest to protect the gut from antibiotics.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39953156},
issn = {1476-4687},
}
RevDate: 2025-02-14
An international perspective on the future of systemic sclerosis research.
Nature reviews. Rheumatology [Epub ahead of print].
Systemic sclerosis (SSc) remains a challenging and enigmatic systemic autoimmune disease, owing to its complex pathogenesis, clinical and molecular heterogeneity, and the lack of effective disease-modifying treatments. Despite a century of research in SSc, the interconnections among microvascular dysfunction, autoimmune phenomena and tissue fibrosis in SSc remain unclear. The absence of validated biomarkers and reliable animal models complicates diagnosis and treatment, contributing to high morbidity and mortality. Advances in the past 5 years, such as single-cell RNA sequencing, next-generation sequencing, spatial biology, transcriptomics, genomics, proteomics, metabolomics, microbiome profiling and artificial intelligence, offer new avenues for identifying the early pathogenetic events that, once treated, could change the clinical history of SSc. Collaborative global efforts to integrate these approaches are crucial to developing a comprehensive, mechanistic understanding and enabling personalized therapies. Challenges include disease classification, clinical heterogeneity and the establishment of robust biomarkers for disease activity and progression. Innovative clinical trial designs and patient-centred approaches are essential for developing effective treatments. Emerging therapies, including cell-based and fibroblast-targeting treatments, show promise. Global cooperation, standardized protocols and interdisciplinary research are vital for advancing SSc research and improving patient outcomes. The integration of advanced research techniques holds the potential for important breakthroughs in the diagnosis, treatment and care of individuals with SSc.
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@article {pmid39953141,
year = {2025},
author = {Abraham, DJ and Black, CM and Denton, CP and Distler, JHW and Domsic, R and Feghali-Bostwick, C and Gourh, P and Hinchcliff, M and Kolling, F and Kuwana, M and Lafyatis, R and Landegren, U and Mahoney, JM and Martin, J and Matucci-Cerinic, M and McMahan, ZH and Mora, AL and Mouthon, L and Rabinovitch, M and Rojas, M and Rubin, K and Trojanowska, M and Varga, J and Whitfield, ML and Gabrielli, A and Krieg, T},
title = {An international perspective on the future of systemic sclerosis research.},
journal = {Nature reviews. Rheumatology},
volume = {},
number = {},
pages = {},
pmid = {39953141},
issn = {1759-4804},
abstract = {Systemic sclerosis (SSc) remains a challenging and enigmatic systemic autoimmune disease, owing to its complex pathogenesis, clinical and molecular heterogeneity, and the lack of effective disease-modifying treatments. Despite a century of research in SSc, the interconnections among microvascular dysfunction, autoimmune phenomena and tissue fibrosis in SSc remain unclear. The absence of validated biomarkers and reliable animal models complicates diagnosis and treatment, contributing to high morbidity and mortality. Advances in the past 5 years, such as single-cell RNA sequencing, next-generation sequencing, spatial biology, transcriptomics, genomics, proteomics, metabolomics, microbiome profiling and artificial intelligence, offer new avenues for identifying the early pathogenetic events that, once treated, could change the clinical history of SSc. Collaborative global efforts to integrate these approaches are crucial to developing a comprehensive, mechanistic understanding and enabling personalized therapies. Challenges include disease classification, clinical heterogeneity and the establishment of robust biomarkers for disease activity and progression. Innovative clinical trial designs and patient-centred approaches are essential for developing effective treatments. Emerging therapies, including cell-based and fibroblast-targeting treatments, show promise. Global cooperation, standardized protocols and interdisciplinary research are vital for advancing SSc research and improving patient outcomes. The integration of advanced research techniques holds the potential for important breakthroughs in the diagnosis, treatment and care of individuals with SSc.},
}
RevDate: 2025-02-14
Response to electroconvulsive therapy is associated with a more diverse oral microbiome- a prospective longitudinal cohort pilot study.
European archives of psychiatry and clinical neuroscience [Epub ahead of print].
Recently it has been shown that psychiatric disorders are associated with changes in the host microbiome. Little is known about the association of electroconvulsive therapy (ECT) and microbiome alterations. In our pilot-study, 15 patients with severe or treatment resistant depression were prospectively recruited and oral swabs were collected pre- and post-ECT. Compared to a control group, ECT did not lead to a significant microbial shift in longitudinal samples (p = 0.65). However, alpha diversity measurements significantly differed between responders and non-responders before ECT (observed species p = 0.014, Shannon p = 0.03) and after ECT (observed species p = 0.015, Shannon p = 0.13).
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@article {pmid39953120,
year = {2025},
author = {Ammer-Herrmenau, C and Hamm, J and Neesse, A and Günther, K and Besse, M and Zilles-Wegner, D},
title = {Response to electroconvulsive therapy is associated with a more diverse oral microbiome- a prospective longitudinal cohort pilot study.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {},
number = {},
pages = {},
pmid = {39953120},
issn = {1433-8491},
abstract = {Recently it has been shown that psychiatric disorders are associated with changes in the host microbiome. Little is known about the association of electroconvulsive therapy (ECT) and microbiome alterations. In our pilot-study, 15 patients with severe or treatment resistant depression were prospectively recruited and oral swabs were collected pre- and post-ECT. Compared to a control group, ECT did not lead to a significant microbial shift in longitudinal samples (p = 0.65). However, alpha diversity measurements significantly differed between responders and non-responders before ECT (observed species p = 0.014, Shannon p = 0.03) and after ECT (observed species p = 0.015, Shannon p = 0.13).},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats.
NPJ biofilms and microbiomes, 11(1):29.
Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.
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Citation:
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@article {pmid39953051,
year = {2025},
author = {Lan, LY and Liu, TC and Gao, SM and Li, Q and Yang, L and Fei, HL and Zhong, XK and Wang, YX and Zhu, CY and Abel, C and Kappeler, PM and Huang, LN and Fan, PF},
title = {Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {29},
pmid = {39953051},
issn = {2055-5008},
support = {32201269//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Hylobates ; *Ecosystem ; *Bacteria/classification/genetics/isolation & purification ; Adaptation, Physiological ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodiversity ; },
abstract = {Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Gastrointestinal Microbiome
Animals
*Hylobates
*Ecosystem
*Bacteria/classification/genetics/isolation & purification
Adaptation, Physiological
RNA, Ribosomal, 16S/genetics
Phylogeny
Biodiversity
RevDate: 2025-02-14
Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.
Trends in plant science pii:S1360-1385(25)00032-9 [Epub ahead of print].
Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.
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@article {pmid39952886,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.01.011},
pmid = {39952886},
issn = {1878-4372},
abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.},
}
RevDate: 2025-02-14
The Lost Kingdom: commensal protists in the gut microbiota.
Trends in microbiology pii:S0966-842X(25)00009-5 [Epub ahead of print].
The gut microbiota critically influences many aspects of host biology, from nutrient acquisition to immunological function, and is integral to metazoan life. While most microbiome research has focused on bacteria, the intestinal microbiota encompasses a diverse constellation of microorganisms, including viruses, fungi, archaea, and protists. Among these microbes, commensal protists have been particularly neglected, to the point that their status as true members of the microbiota remained contentious. However, findings over the past decade revealed that commensal protists, particularly those in the Parabasalia phylum (parabasalids), perform keystone roles within the intestinal ecosystem. Emerging evidence highlights how parabasalids dramatically impact host immunity, gut microbiome ecology, and host susceptibility to both infectious and inflammatory diseases. In this review, we discuss the recent discoveries of the varied and powerful roles of commensal parabasalids in the intestinal microbiota and outline the challenges and opportunities in this burgeoning new area of the microbiome field.
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@article {pmid39952813,
year = {2025},
author = {Gerrick, ER and Howitt, MR},
title = {The Lost Kingdom: commensal protists in the gut microbiota.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.01.008},
pmid = {39952813},
issn = {1878-4380},
abstract = {The gut microbiota critically influences many aspects of host biology, from nutrient acquisition to immunological function, and is integral to metazoan life. While most microbiome research has focused on bacteria, the intestinal microbiota encompasses a diverse constellation of microorganisms, including viruses, fungi, archaea, and protists. Among these microbes, commensal protists have been particularly neglected, to the point that their status as true members of the microbiota remained contentious. However, findings over the past decade revealed that commensal protists, particularly those in the Parabasalia phylum (parabasalids), perform keystone roles within the intestinal ecosystem. Emerging evidence highlights how parabasalids dramatically impact host immunity, gut microbiome ecology, and host susceptibility to both infectious and inflammatory diseases. In this review, we discuss the recent discoveries of the varied and powerful roles of commensal parabasalids in the intestinal microbiota and outline the challenges and opportunities in this burgeoning new area of the microbiome field.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Exploring viral diversity in fermented vegetables through viral metagenomics.
Food microbiology, 128:104733.
Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.
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@article {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}
MeSH Terms:
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*Metagenomics
*Vegetables/virology/microbiology
*Fermentation
*Bacteriophages/genetics/isolation & purification/classification
Microbiota
Brassica/microbiology/virology
Fermented Foods/microbiology/virology
Bacteria/genetics/classification/isolation & purification/virology
Biodiversity
Daucus carota/microbiology/virology
Food Microbiology
Viruses/isolation & purification/classification/genetics
Enterobacteriaceae/isolation & purification/genetics/virology/classification
Metagenome
Lactobacillaceae/isolation & purification/genetics/classification
RevDate: 2025-02-14
CmpDate: 2025-02-14
Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.
Food microbiology, 128:104734.
Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.
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@article {pmid39952751,
year = {2025},
author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F},
title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104734},
doi = {10.1016/j.fm.2025.104734},
pmid = {39952751},
issn = {1095-9998},
mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; },
abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Chickens/microbiology
*Food Storage
Poultry Products/microbiology
Food Packaging/methods
Food Microbiology
Poultry/microbiology
Drug Resistance, Bacterial
Temperature
Meat/microbiology
Brochothrix/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Environmental Microbiology
Metagenomics
RevDate: 2025-02-14
The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.
Insect molecular biology [Epub ahead of print].
Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.
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@article {pmid39952648,
year = {2025},
author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G},
title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12983},
pmid = {39952648},
issn = {1365-2583},
support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; },
abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.},
}
RevDate: 2025-02-14
Holistic Assessment of Chemical and Biological Pollutants in a Mediterranean Wastewater Effluent-Dominated Stream: Interactions and Ecological Impacts.
Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(25)00206-4 [Epub ahead of print].
The discharge of treated wastewater from wastewater treatment plants (WWTPs) into river systems is a significant source of pollution, introducing a range of chemical and biological pollutants that impact the chemical and ecological quality status of rivers. This study evaluates the effect of a secondary treated wastewater effluent on the Onyar River, in the northeast Spain. Water and biofilm samples were collected at one upstream and four downstream sampling points (up to 2.8 km from the discharge point) across four seasons. A wide array of pollutants, including metals, pharmaceuticals, microplastics (MPs), per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), among other emerging pollutants, were detected downstream, with significant differences between upstream and downstream concentrations. Our results show that WWTP discharge also altered biofilm microbiome composition and ARGs presence, being these changes distinguishable from seasonal variations. Nevertheless, a partial recovery further downstream (525 m) was observed for biofilm microbiome and ARGs composition. These findings highlight the value of microbiome analysis in assessing wastewater impacts on river ecosystems and emphasize the need for further research to improve pollutant attenuation and biofilm recovery strategies in river streams.
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@article {pmid39952585,
year = {2025},
author = {Marizzi Del Olmo, A and López-Doval, JC and Hidalgo, M and Serra, T and Colomer, J and Salvadó, V and Casas, ME and Medina, JS and Matamoros, V},
title = {Holistic Assessment of Chemical and Biological Pollutants in a Mediterranean Wastewater Effluent-Dominated Stream: Interactions and Ecological Impacts.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125833},
doi = {10.1016/j.envpol.2025.125833},
pmid = {39952585},
issn = {1873-6424},
abstract = {The discharge of treated wastewater from wastewater treatment plants (WWTPs) into river systems is a significant source of pollution, introducing a range of chemical and biological pollutants that impact the chemical and ecological quality status of rivers. This study evaluates the effect of a secondary treated wastewater effluent on the Onyar River, in the northeast Spain. Water and biofilm samples were collected at one upstream and four downstream sampling points (up to 2.8 km from the discharge point) across four seasons. A wide array of pollutants, including metals, pharmaceuticals, microplastics (MPs), per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), among other emerging pollutants, were detected downstream, with significant differences between upstream and downstream concentrations. Our results show that WWTP discharge also altered biofilm microbiome composition and ARGs presence, being these changes distinguishable from seasonal variations. Nevertheless, a partial recovery further downstream (525 m) was observed for biofilm microbiome and ARGs composition. These findings highlight the value of microbiome analysis in assessing wastewater impacts on river ecosystems and emphasize the need for further research to improve pollutant attenuation and biofilm recovery strategies in river streams.},
}
RevDate: 2025-02-14
Research progress on edible mushroom polysaccharides as a novel therapeutic strategy for inflammatory bowel disease.
International journal of biological macromolecules pii:S0141-8130(25)01543-0 [Epub ahead of print].
Inflammatory bowel disease (IBD) is a complex condition linked to the gut microbiota, host metabolism, and the immune system. Edible mushroom polysaccharides (EMPs) are gaining attention for their benefits, particularly as prebiotics that help balance gut microbial, a key factor in IBD. With their scalable production, diverse hydrophilic properties, and demonstrated anti-inflammatory effects in both laboratory and animal studies, EMPs show promise for easing IBD symptoms. By supporting a healthy gut microbiome through various mechanisms, EMPs can play an important role in preventing and managing IBD, ultimately benefiting overall health and opening new treatment avenues. This review examines how EMPs affect IBD, focusing on their role in shaping gut microbiota, restoring gut barriers, regulating immune function, and influencing pathways related to colitis. It also explores their impact on the microbiota-gut-multi organ axis and overall host health, as well as the relationship between EMPs preparation, structure, and bioactivity, along with their potential applications in food and medicine. This investigation provides valuable insights into the intricate connections between the gut, immune system, and systemic inflammation system, highlighting how EMPs are key players in this complex interaction.
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@article {pmid39952533,
year = {2025},
author = {Song, Y and Feng, Y and Liu, G and Duan, Y and Zhang, H},
title = {Research progress on edible mushroom polysaccharides as a novel therapeutic strategy for inflammatory bowel disease.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {140994},
doi = {10.1016/j.ijbiomac.2025.140994},
pmid = {39952533},
issn = {1879-0003},
abstract = {Inflammatory bowel disease (IBD) is a complex condition linked to the gut microbiota, host metabolism, and the immune system. Edible mushroom polysaccharides (EMPs) are gaining attention for their benefits, particularly as prebiotics that help balance gut microbial, a key factor in IBD. With their scalable production, diverse hydrophilic properties, and demonstrated anti-inflammatory effects in both laboratory and animal studies, EMPs show promise for easing IBD symptoms. By supporting a healthy gut microbiome through various mechanisms, EMPs can play an important role in preventing and managing IBD, ultimately benefiting overall health and opening new treatment avenues. This review examines how EMPs affect IBD, focusing on their role in shaping gut microbiota, restoring gut barriers, regulating immune function, and influencing pathways related to colitis. It also explores their impact on the microbiota-gut-multi organ axis and overall host health, as well as the relationship between EMPs preparation, structure, and bioactivity, along with their potential applications in food and medicine. This investigation provides valuable insights into the intricate connections between the gut, immune system, and systemic inflammation system, highlighting how EMPs are key players in this complex interaction.},
}
RevDate: 2025-02-14
Metatranscriptomics reveals that plant tannins regulate the expression of intestinal antibiotic resistance genes in Qinghai voles (Neodon fuscus).
Environmental research pii:S0013-9351(25)00370-6 [Epub ahead of print].
Antibiotic resistance genes (ARGs) are a persistent harmful environmental pollutant, epidemic of ARGs thought to be a result of antibiotic misuse. Tannin acid (TA) is a natural plant compounds with bactericidal properties. Nowadays, TA is considered to be a potential replacement of antibiotics. However, the role of TA on ARGs is also not yet clear. To address this knowledge gap, we fed the model plateau animal Qinghai voles (Neodon fuscus) with different concentration TA. We used 16S rDNA sequencing for revealing total bacteria, 16S rRNA sequencing for revealing active bacteria, and metatranscriptomics (active function) sequencing for revealing ARGs and other functions under different TA. Our results showed that although TA reduced macrolide ARGs, TA group enriched 6-fold for tetracycline ARGs, 3-fold for multidrug ARGs, and 5-fold for aminoglycoside ARGs compared with control group. Moreover, TA reduced animal growth performance, and regulated gut microbiome more stable by improving microbial diversity. And TA promoted the production of short-chain fatty acids by gut microbes, such as lactate and acetate. This study reveals modulation of ARGs and gut microbiome by TA and also provides scientific value for the proper use of TA in feed and medical treatment.
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@article {pmid39952456,
year = {2025},
author = {Shi, S and Gan, X and Qian, Y and Cao, Y and Wang, Y and Shi, C and Bi, J and Yu, Q and Han, Q and Qu, J and Li, H},
title = {Metatranscriptomics reveals that plant tannins regulate the expression of intestinal antibiotic resistance genes in Qinghai voles (Neodon fuscus).},
journal = {Environmental research},
volume = {},
number = {},
pages = {121119},
doi = {10.1016/j.envres.2025.121119},
pmid = {39952456},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) are a persistent harmful environmental pollutant, epidemic of ARGs thought to be a result of antibiotic misuse. Tannin acid (TA) is a natural plant compounds with bactericidal properties. Nowadays, TA is considered to be a potential replacement of antibiotics. However, the role of TA on ARGs is also not yet clear. To address this knowledge gap, we fed the model plateau animal Qinghai voles (Neodon fuscus) with different concentration TA. We used 16S rDNA sequencing for revealing total bacteria, 16S rRNA sequencing for revealing active bacteria, and metatranscriptomics (active function) sequencing for revealing ARGs and other functions under different TA. Our results showed that although TA reduced macrolide ARGs, TA group enriched 6-fold for tetracycline ARGs, 3-fold for multidrug ARGs, and 5-fold for aminoglycoside ARGs compared with control group. Moreover, TA reduced animal growth performance, and regulated gut microbiome more stable by improving microbial diversity. And TA promoted the production of short-chain fatty acids by gut microbes, such as lactate and acetate. This study reveals modulation of ARGs and gut microbiome by TA and also provides scientific value for the proper use of TA in feed and medical treatment.},
}
RevDate: 2025-02-14
The impact of gut microbiota on the occurrence, treatment, and prognosis of ischemic stroke.
Neurobiology of disease pii:S0969-9961(25)00052-X [Epub ahead of print].
Ischemic stroke (IS) is a cerebrovascular disease that predominantly affects middle-aged and elderly populations, exhibiting high mortality and disability rates. At present, the incidence of IS is increasing annually, with a notable trend towards younger affected individuals. Recent discoveries concerning the "gut-brain axis" have established a connection between the gut and the brain. Numerous studies have revealed that intestinal microbes play a crucial role in the onset, progression, and outcomes of IS. They are involved in the entire pathophysiological process of IS through mechanisms such as chronic inflammation, neural regulation, and metabolic processes. Although numerous studies have explored the relationship between IS and intestinal microbiota, comprehensive analyses of specific microbiota is relatively scarce. Therefore, this paper provides an overview of the typical changes in gut microbiota following IS and investigates the role of specific microorganisms in this context. Additionally, it presents a comprehensive analysis of post-stroke microbiological therapy and the relationship between IS and diet. The aim is to identify potential microbial targets for therapeutic intervention, as well as to highlight the benefits of microbiological therapies and the significance of dietary management. Overall, this paper seeks to provide key strategies for the treatment and management of IS, advocating for healthy diets and health programs for individuals. Meanwhile, it may offer a new perspective on the future interdisciplinary development of neurology, microbiology and nutrition.
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@article {pmid39952411,
year = {2025},
author = {Chen, L and Wang, X and Wang, S and Liu, W and Song, Z and Liao, H},
title = {The impact of gut microbiota on the occurrence, treatment, and prognosis of ischemic stroke.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {106836},
doi = {10.1016/j.nbd.2025.106836},
pmid = {39952411},
issn = {1095-953X},
abstract = {Ischemic stroke (IS) is a cerebrovascular disease that predominantly affects middle-aged and elderly populations, exhibiting high mortality and disability rates. At present, the incidence of IS is increasing annually, with a notable trend towards younger affected individuals. Recent discoveries concerning the "gut-brain axis" have established a connection between the gut and the brain. Numerous studies have revealed that intestinal microbes play a crucial role in the onset, progression, and outcomes of IS. They are involved in the entire pathophysiological process of IS through mechanisms such as chronic inflammation, neural regulation, and metabolic processes. Although numerous studies have explored the relationship between IS and intestinal microbiota, comprehensive analyses of specific microbiota is relatively scarce. Therefore, this paper provides an overview of the typical changes in gut microbiota following IS and investigates the role of specific microorganisms in this context. Additionally, it presents a comprehensive analysis of post-stroke microbiological therapy and the relationship between IS and diet. The aim is to identify potential microbial targets for therapeutic intervention, as well as to highlight the benefits of microbiological therapies and the significance of dietary management. Overall, this paper seeks to provide key strategies for the treatment and management of IS, advocating for healthy diets and health programs for individuals. Meanwhile, it may offer a new perspective on the future interdisciplinary development of neurology, microbiology and nutrition.},
}
RevDate: 2025-02-14
Gut-Joint Axis: History of Clostridium Difficile Infection Increases the Risk of Periprosthetic Joint Infection After Total Knee Arthroplasty.
The Journal of arthroplasty pii:S0883-5403(25)00142-1 [Epub ahead of print].
INTRODUCTION: Increasing evidence suggests that the gut microbiome is important in immune system function and influences the risk of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA). A C. difficile infection (CDI) is an indicator of poor gut microbiome health. However, no prior studies have evaluated the independent risk of CDI on the rates of PJI after TKA.
METHODS: Patients undergoing TKA from 2010 to 2021 were identified in a patient claims database (n = 1,416,362). Patients who had a history of CDI within two years prior to TKA (n = 5,170) were propensity-matched on a 1:4 basis to those who did not have a diagnosis of CDI. The exposed CDI cohort was also stratified into four groups by time of CDI before TKA (zero to three months, three to six months, six to 12 months, and one to two years). The risk of PJI within two years following TKA was compared between the exposed and control cohorts. Logistic regression was used to evaluate the association of CDI occurring in each time interval prior to TKA and PJI after TKA.
RESULTS: A CDI within two years prior to TKA was independently associated with higher odds of PJI (OR [odds ratio], 2.1; 95% CI [confidence interval], 1.91 to 2.36). In addition, we observed a stepwise increase in the risk of PJI by the timing of preoperative CDI infection, with patients who had a diagnosis of CDI within three months of their primary TKA exhibiting the highest odds of developing PJI (OR, 4.19; 95% CI, 3.51 to 5.02). Additionally, patients who had a diagnosis of CDI within two years of undergoing primary TKA were significantly more likely to experience a subsequent episode of CDI at the latest follow-up (OR, 25.9; 95% CI, 22.3 to 30.1).
CONCLUSION: A CDI prior to TKA is an independent risk factor for PJI. Closer proximity of CDI to surgery is associated with a "dose-dependent" increased PJI risk. Surgeons should consider delaying TKA until a minimum of one year after a diagnosis of CDI.
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@article {pmid39952304,
year = {2025},
author = {Verhey, JT and Boddu, SP and Tarabichi, S and Deckey, DG and Christopher, ZK and Spangehl, MJ and Clarke, HD and Bingham, JS},
title = {Gut-Joint Axis: History of Clostridium Difficile Infection Increases the Risk of Periprosthetic Joint Infection After Total Knee Arthroplasty.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.02.014},
pmid = {39952304},
issn = {1532-8406},
abstract = {INTRODUCTION: Increasing evidence suggests that the gut microbiome is important in immune system function and influences the risk of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA). A C. difficile infection (CDI) is an indicator of poor gut microbiome health. However, no prior studies have evaluated the independent risk of CDI on the rates of PJI after TKA.
METHODS: Patients undergoing TKA from 2010 to 2021 were identified in a patient claims database (n = 1,416,362). Patients who had a history of CDI within two years prior to TKA (n = 5,170) were propensity-matched on a 1:4 basis to those who did not have a diagnosis of CDI. The exposed CDI cohort was also stratified into four groups by time of CDI before TKA (zero to three months, three to six months, six to 12 months, and one to two years). The risk of PJI within two years following TKA was compared between the exposed and control cohorts. Logistic regression was used to evaluate the association of CDI occurring in each time interval prior to TKA and PJI after TKA.
RESULTS: A CDI within two years prior to TKA was independently associated with higher odds of PJI (OR [odds ratio], 2.1; 95% CI [confidence interval], 1.91 to 2.36). In addition, we observed a stepwise increase in the risk of PJI by the timing of preoperative CDI infection, with patients who had a diagnosis of CDI within three months of their primary TKA exhibiting the highest odds of developing PJI (OR, 4.19; 95% CI, 3.51 to 5.02). Additionally, patients who had a diagnosis of CDI within two years of undergoing primary TKA were significantly more likely to experience a subsequent episode of CDI at the latest follow-up (OR, 25.9; 95% CI, 22.3 to 30.1).
CONCLUSION: A CDI prior to TKA is an independent risk factor for PJI. Closer proximity of CDI to surgery is associated with a "dose-dependent" increased PJI risk. Surgeons should consider delaying TKA until a minimum of one year after a diagnosis of CDI.},
}
RevDate: 2025-02-14
Changes in gut microbiota affect DNA methylation levels and development of chicken muscle tissue.
Poultry science, 104(3):104869 pii:S0032-5791(25)00106-3 [Epub ahead of print].
The intestinal microbiome is essential in regulating host muscle growth and development. Antibiotic treatment is commonly used to model dysbiosis of the intestinal microbiota, yet limited research addresses the relationship between gut microbes and muscle growth in yellow-feathered broilers. In this study, Xinghua chickens were administered broad-spectrum antibiotics for eight weeks to induce gut microbiome suppression. We investigated the relationships between the gut microbiome and muscle growth using 16S rRNA sequencing and transcriptomic analysis. Results indicated that antibiotic treatment significantly reduced body weight, dressed weight, eviscerated weight, and breast and leg muscle weight. Microbial diversity and richness in the duodenum, jejunum, ileum, and cecum were significantly decreased. The relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes declined, while Proteobacteria increased. This microbial imbalance led to 298 differentially expressed genes (DEGs) in muscle tissue, of which 67 down-regulated genes were enriched in skeletal muscle development, including MYF6, MYBPC1 and METTL21C genes essential for muscle development. The DEGs were primarily involved in the MAPK signaling pathway, calcium signaling pathway, ECM-receptor interaction, actin cytoskeleton regulation, and nitrogen metabolism. Correlation analysis showed that dysregulation of the cecal microbiome had the most substantial effect on muscle growth and development. Furthermore, intestinal microbiome dysregulation reduced DNMT3b and METTL21C mRNA expression in muscle tissue, lowered overall DNA methylation and SAM levels, and induced methylation changes that impacted skeletal muscle development. This study demonstrates that gut microbiota influence DNA methylation in muscle tissue, thereby associated with muscle growth and development.
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@article {pmid39952142,
year = {2025},
author = {Xu, Y and Huang, Y and Wei, S and Tian, J and Huang, Y and Nie, Q and Zhang, D},
title = {Changes in gut microbiota affect DNA methylation levels and development of chicken muscle tissue.},
journal = {Poultry science},
volume = {104},
number = {3},
pages = {104869},
doi = {10.1016/j.psj.2025.104869},
pmid = {39952142},
issn = {1525-3171},
abstract = {The intestinal microbiome is essential in regulating host muscle growth and development. Antibiotic treatment is commonly used to model dysbiosis of the intestinal microbiota, yet limited research addresses the relationship between gut microbes and muscle growth in yellow-feathered broilers. In this study, Xinghua chickens were administered broad-spectrum antibiotics for eight weeks to induce gut microbiome suppression. We investigated the relationships between the gut microbiome and muscle growth using 16S rRNA sequencing and transcriptomic analysis. Results indicated that antibiotic treatment significantly reduced body weight, dressed weight, eviscerated weight, and breast and leg muscle weight. Microbial diversity and richness in the duodenum, jejunum, ileum, and cecum were significantly decreased. The relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes declined, while Proteobacteria increased. This microbial imbalance led to 298 differentially expressed genes (DEGs) in muscle tissue, of which 67 down-regulated genes were enriched in skeletal muscle development, including MYF6, MYBPC1 and METTL21C genes essential for muscle development. The DEGs were primarily involved in the MAPK signaling pathway, calcium signaling pathway, ECM-receptor interaction, actin cytoskeleton regulation, and nitrogen metabolism. Correlation analysis showed that dysregulation of the cecal microbiome had the most substantial effect on muscle growth and development. Furthermore, intestinal microbiome dysregulation reduced DNMT3b and METTL21C mRNA expression in muscle tissue, lowered overall DNA methylation and SAM levels, and induced methylation changes that impacted skeletal muscle development. This study demonstrates that gut microbiota influence DNA methylation in muscle tissue, thereby associated with muscle growth and development.},
}
RevDate: 2025-02-14
Dichotomous effects of Galectin-9 in disease modulation in murine models of inflammatory bowel disease.
Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 184:117902 pii:S0753-3322(25)00096-4 [Epub ahead of print].
Inflammatory bowel disease (IBD) is a multifaceted disease characterised by compromised integrity of the epithelial barrier, the gut microbiome, and mucosal inflammation. While leukocyte recruitment and infiltration into intestinal tissue are well-studied and targeted in clinical practice, the role of galectins in modulating mucosal immunity remains underexplored. Galectins, a family of lectin-binding proteins, mediate critical interactions between immune cells and the intestinal epithelium. This study investigated the effect of endogenous Galectin-9 (Gal-9), as well as the combined effects with Galectin-3 (Gal-3), in modulating disease progression in murine models of colitis, using global knockout (KO) models for Gal-3, Gal-9, and Gal-3/Gal-9. Global deficiency in both galectins demonstrated improved disease parameters in Dextran sodium sulfate (DSS)-driven colitis. In contrast, in a model of adoptive T cell driven colitis, the addition of recombinant Gal-9 (rGal-9) was associated with reduced intestinal inflammation and an improvement in disease parameters. Further in vitro studies revealed no change in bone marrow-derived macrophage cytokine production in the absence of endogenous Gal-9, whereas the addition of rGal-9 to human macrophages stimulated pro-inflammatory cytokine production. Collectively, these findings demonstrate that Gal-9 plays distinct, context-dependent effects in intestinal inflammation, with both pro-inflammatory and anti-inflammatory effects. The contrasting functions of endogenous and exogenous Gal-9 underscore its complex involvement in IBD pathogenesis and highlight the need to differentiate its physiological function from therapeutic applications.
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@article {pmid39951917,
year = {2025},
author = {Tull, S and Saviano, A and Fatima, A and Begum, J and Mansour, AA and Marigliano, N and Schettino, A and Blaising, J and Trenkle, P and Sandrin, V and Maione, F and Regan-Komito, D and Iqbal, AJ},
title = {Dichotomous effects of Galectin-9 in disease modulation in murine models of inflammatory bowel disease.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {184},
number = {},
pages = {117902},
doi = {10.1016/j.biopha.2025.117902},
pmid = {39951917},
issn = {1950-6007},
abstract = {Inflammatory bowel disease (IBD) is a multifaceted disease characterised by compromised integrity of the epithelial barrier, the gut microbiome, and mucosal inflammation. While leukocyte recruitment and infiltration into intestinal tissue are well-studied and targeted in clinical practice, the role of galectins in modulating mucosal immunity remains underexplored. Galectins, a family of lectin-binding proteins, mediate critical interactions between immune cells and the intestinal epithelium. This study investigated the effect of endogenous Galectin-9 (Gal-9), as well as the combined effects with Galectin-3 (Gal-3), in modulating disease progression in murine models of colitis, using global knockout (KO) models for Gal-3, Gal-9, and Gal-3/Gal-9. Global deficiency in both galectins demonstrated improved disease parameters in Dextran sodium sulfate (DSS)-driven colitis. In contrast, in a model of adoptive T cell driven colitis, the addition of recombinant Gal-9 (rGal-9) was associated with reduced intestinal inflammation and an improvement in disease parameters. Further in vitro studies revealed no change in bone marrow-derived macrophage cytokine production in the absence of endogenous Gal-9, whereas the addition of rGal-9 to human macrophages stimulated pro-inflammatory cytokine production. Collectively, these findings demonstrate that Gal-9 plays distinct, context-dependent effects in intestinal inflammation, with both pro-inflammatory and anti-inflammatory effects. The contrasting functions of endogenous and exogenous Gal-9 underscore its complex involvement in IBD pathogenesis and highlight the need to differentiate its physiological function from therapeutic applications.},
}
RevDate: 2025-02-14
An in silico framework for the rational design of vaginal probiotic therapy.
PLoS computational biology, 21(2):e1012064 pii:PCOMPBIOL-D-24-00604 [Epub ahead of print].
Bacterial vaginosis (BV) is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop an in silico framework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This computational framework highlighted the importance of resident microbial species on the efficacy of hypothetical probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) and Lactobacillus spp. with candidate probiotic strains as a necessary selection criterion. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of the in silico platform. Results from the computational model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.
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@article {pmid39951429,
year = {2025},
author = {Lee, CY and Bonakdar, S and Arnold, KB},
title = {An in silico framework for the rational design of vaginal probiotic therapy.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012064},
doi = {10.1371/journal.pcbi.1012064},
pmid = {39951429},
issn = {1553-7358},
abstract = {Bacterial vaginosis (BV) is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop an in silico framework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This computational framework highlighted the importance of resident microbial species on the efficacy of hypothetical probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) and Lactobacillus spp. with candidate probiotic strains as a necessary selection criterion. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of the in silico platform. Results from the computational model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.
PloS one, 20(2):e0306503 pii:PONE-D-24-24820.
The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.
Additional Links: PMID-39951402
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PubMed:
Citation:
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@article {pmid39951402,
year = {2025},
author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M},
title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0306503},
doi = {10.1371/journal.pone.0306503},
pmid = {39951402},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; },
abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Biodegradation, Environmental
*Groundwater/microbiology
*Metagenome
*Tetrachloroethylene/metabolism
Water Pollutants, Chemical/metabolism
Halogenation
Metagenomics/methods
Bacteria/genetics/metabolism/classification
New Mexico
RevDate: 2025-02-14
Hormonal Birth Control Is Associated with Altered Gut Microbiota Beta-Diversity in Physically Active Females Across the Menstrual Cycle: A Pilot Trial.
Journal of applied physiology (Bethesda, Md. : 1985) [Epub ahead of print].
Understanding changes to gut microbiota composition in response to hormonal birth control (HBC) may provide insight into the microbial mechanisms underlying the metabolic effects of HBC, for example, altered short-chain fatty acid (SCFA) production. Athletes' unique physiological demands may interact with these microbial mechanisms in distinct ways; however, there is limited research on HBC and gut microbiota diversity and composition across different menstrual cycle phases in physically active females. A pilot cohort of physically active females using HBC (oral contraceptives, hormone-based intrauterine devices, or arm implants) and a control group not using HBC (n=12 per group; 22±2yrs, 24±4kg/m[2] vs. 22±4yrs, 23±4kg/m[2]; Ps≥0.496) provided fecal samples alongside self-reported menstrual phase and circulating sex hormones. Alpha diversity (microbial richness and evenness) was assessed using Shannon Index while beta-diversity (microbial composition differences) was analyzed using PERMANOVA based on Bray-Curtis dissimilarity. Circulating estrogen and luteinizing hormone increased from early (days 1-5) to mid-cycle (days 12-17) in both groups (time effect Ps≤0.01), with greater changes in Control (Ps≤0.046) than HBC (Ps≥0.231). While no menstrual phase effect was observed on either diversity measure (Ps≥0.473), beta-diversity differed between Control and HBC groups (P=0.015), reflecting distinct gut microbiota profiles irrespective of menstrual phase. Seven taxa linked to SCFA production were less abundant in the HBC group (unadjusted Ps≤0.046), though significance was lost after adjusting for multiple comparisons. These findings suggest that in physically active females, hormonal contraception influences gut microbial composition, which may have downstream effects on metabolism and performance.
Additional Links: PMID-39951399
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PubMed:
Citation:
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@article {pmid39951399,
year = {2025},
author = {Brito, J and Grosicki, GJ and Robinson, AT and Coburn, JW and Costa, PB and Holmes, KE and Lyon, G and Hakonsson, Z and Conti, F and Galpin, AJ},
title = {Hormonal Birth Control Is Associated with Altered Gut Microbiota Beta-Diversity in Physically Active Females Across the Menstrual Cycle: A Pilot Trial.},
journal = {Journal of applied physiology (Bethesda, Md. : 1985)},
volume = {},
number = {},
pages = {},
doi = {10.1152/japplphysiol.00008.2025},
pmid = {39951399},
issn = {1522-1601},
abstract = {Understanding changes to gut microbiota composition in response to hormonal birth control (HBC) may provide insight into the microbial mechanisms underlying the metabolic effects of HBC, for example, altered short-chain fatty acid (SCFA) production. Athletes' unique physiological demands may interact with these microbial mechanisms in distinct ways; however, there is limited research on HBC and gut microbiota diversity and composition across different menstrual cycle phases in physically active females. A pilot cohort of physically active females using HBC (oral contraceptives, hormone-based intrauterine devices, or arm implants) and a control group not using HBC (n=12 per group; 22±2yrs, 24±4kg/m[2] vs. 22±4yrs, 23±4kg/m[2]; Ps≥0.496) provided fecal samples alongside self-reported menstrual phase and circulating sex hormones. Alpha diversity (microbial richness and evenness) was assessed using Shannon Index while beta-diversity (microbial composition differences) was analyzed using PERMANOVA based on Bray-Curtis dissimilarity. Circulating estrogen and luteinizing hormone increased from early (days 1-5) to mid-cycle (days 12-17) in both groups (time effect Ps≤0.01), with greater changes in Control (Ps≤0.046) than HBC (Ps≥0.231). While no menstrual phase effect was observed on either diversity measure (Ps≥0.473), beta-diversity differed between Control and HBC groups (P=0.015), reflecting distinct gut microbiota profiles irrespective of menstrual phase. Seven taxa linked to SCFA production were less abundant in the HBC group (unadjusted Ps≤0.046), though significance was lost after adjusting for multiple comparisons. These findings suggest that in physically active females, hormonal contraception influences gut microbial composition, which may have downstream effects on metabolism and performance.},
}
RevDate: 2025-02-14
Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression.
Inflammatory bowel diseases pii:8015534 [Epub ahead of print].
BACKGROUND: Crohn's disease (CD) is characterized by an inflammatory response to gut microbiota. Macrophages and dendritic cells play an active role in CD inflammation. Specific microbiota have been implicated in the pathogenesis of ileal CD. We investigated the phagocyte-associated microbiome using an unbiased sequencing approach to identify potential pathobionts and elucidate the host response to these microbes.
METHODS: We collected ileal and colonic mucosal biopsies from CD patients and controls without inflammatory bowel disease (IBD), isolated lamina propria phagocytes (CD11b+ cells), and performed deep RNA sequencing (n = 37). Reads were mapped to the human genome for host gene expression analysis and a prokaryotic database for microbiome taxonomic and metatranscriptomic profiling. Results were confirmed in a second IBD cohort (n = 17). Lysed lamina propria cells were plated for bacterial culturing; isolated colonies underwent whole genome sequencing (n = 11).
RESULTS: Crohn's disease ileal phagocytes contained higher relative abundances of Escherichia coli, Ruminococcus gnavus, and Enterocloster spp. than those from controls. CD phagocyte-associated microbes had increased expression of lipopolysaccharide (LPS) biosynthesis pathways. Phagocytes with a higher pathobiont burden showed increased expression of pro-inflammatory and antimicrobial genes, including PI3 (antimicrobial peptide) and BPIFB1 (LPS-binding molecule). E. coli isolated from the CD lamina propria had more flagellar motility and antibiotic resistance genes than control-derived strains.
CONCLUSIONS: Lamina propria resident phagocytes harbor bacterial strains that may act as pathobionts in CD. Our findings shed light on the role of pathobionts and the immune response in CD pathogenesis and suggest new targets for therapies.
Additional Links: PMID-39951038
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PubMed:
Citation:
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@article {pmid39951038,
year = {2025},
author = {Jacobsen, GE and Gonzalez, EE and Mendygral, P and Faust, KM and Hazime, H and Fernandez, I and Santander, AM and Quintero, MA and Jiang, C and Damas, OM and Deshpande, AR and Kerman, DH and Proksell, S and Sendszichew Shane, M and Sussman, DA and Ghaddar, B and Cickovsk, T and Abreu, MT},
title = {Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae316},
pmid = {39951038},
issn = {1536-4844},
support = {R01DK099076/DK/NIDDK NIH HHS/United States ; T32AI162624//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by an inflammatory response to gut microbiota. Macrophages and dendritic cells play an active role in CD inflammation. Specific microbiota have been implicated in the pathogenesis of ileal CD. We investigated the phagocyte-associated microbiome using an unbiased sequencing approach to identify potential pathobionts and elucidate the host response to these microbes.
METHODS: We collected ileal and colonic mucosal biopsies from CD patients and controls without inflammatory bowel disease (IBD), isolated lamina propria phagocytes (CD11b+ cells), and performed deep RNA sequencing (n = 37). Reads were mapped to the human genome for host gene expression analysis and a prokaryotic database for microbiome taxonomic and metatranscriptomic profiling. Results were confirmed in a second IBD cohort (n = 17). Lysed lamina propria cells were plated for bacterial culturing; isolated colonies underwent whole genome sequencing (n = 11).
RESULTS: Crohn's disease ileal phagocytes contained higher relative abundances of Escherichia coli, Ruminococcus gnavus, and Enterocloster spp. than those from controls. CD phagocyte-associated microbes had increased expression of lipopolysaccharide (LPS) biosynthesis pathways. Phagocytes with a higher pathobiont burden showed increased expression of pro-inflammatory and antimicrobial genes, including PI3 (antimicrobial peptide) and BPIFB1 (LPS-binding molecule). E. coli isolated from the CD lamina propria had more flagellar motility and antibiotic resistance genes than control-derived strains.
CONCLUSIONS: Lamina propria resident phagocytes harbor bacterial strains that may act as pathobionts in CD. Our findings shed light on the role of pathobionts and the immune response in CD pathogenesis and suggest new targets for therapies.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.
Liver international : official journal of the International Association for the Study of the Liver, 45(3):e70023.
BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.
METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.
RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).
CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.
Additional Links: PMID-39950834
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PubMed:
Citation:
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@article {pmid39950834,
year = {2025},
author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS},
title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {3},
pages = {e70023},
doi = {10.1111/liv.70023},
pmid = {39950834},
issn = {1478-3231},
support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; },
abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.
METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.
RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).
CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Glucosides/therapeutic use
Middle Aged
Prospective Studies
*Benzhydryl Compounds/therapeutic use
Non-alcoholic Fatty Liver Disease/drug therapy/microbiology
Treatment Outcome
Magnetic Resonance Imaging
Feces/microbiology
Sodium-Glucose Transporter 2 Inhibitors/therapeutic use
Logistic Models
RevDate: 2025-02-14
Sexually transmitted human papillomavirus and related sequelae.
Clinical microbiology reviews [Epub ahead of print].
SUMMARYMore than 40 types of sexually transmitted human papillomavirus (HPV) infect the oropharyngeal and anogenital mucosa-high-risk types are associated with precancerous and cancerous lesions of the cervix, vagina, vulva, penis, anus, and oropharynx, and low-risk types cause non-malignant disease, such as anogenital warts. Though most HPV infections resolve spontaneously, immunodeficiencies may result in persistent infection and increased risk of HPV-related sequelae. The mechanism by which HPV results in malignant transformation is multifaceted, involving interactions with numerous cellular pathways, the host immune system, and potentially the host microbiome. Vaccination against HPV is highly efficacious in the prevention of infection and related sequelae, and there now exist several approved formulations that protect against both high- and low-risk types. Despite the advent of vaccination, early detection and treatment of cervical and anal precancerous lesions continues to be integral to secondary prevention-molecular HPV testing, cytology, and tissue biopsy allow for triaging of patients, after which appropriate treatment with close follow-up can avert cancer development.
Additional Links: PMID-39950806
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PubMed:
Citation:
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@article {pmid39950806,
year = {2025},
author = {Hanft, W and Stankiewicz Karita, H and Khorsandi, N and Vohra, P and Plotzker, R},
title = {Sexually transmitted human papillomavirus and related sequelae.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0008523},
doi = {10.1128/cmr.00085-23},
pmid = {39950806},
issn = {1098-6618},
abstract = {SUMMARYMore than 40 types of sexually transmitted human papillomavirus (HPV) infect the oropharyngeal and anogenital mucosa-high-risk types are associated with precancerous and cancerous lesions of the cervix, vagina, vulva, penis, anus, and oropharynx, and low-risk types cause non-malignant disease, such as anogenital warts. Though most HPV infections resolve spontaneously, immunodeficiencies may result in persistent infection and increased risk of HPV-related sequelae. The mechanism by which HPV results in malignant transformation is multifaceted, involving interactions with numerous cellular pathways, the host immune system, and potentially the host microbiome. Vaccination against HPV is highly efficacious in the prevention of infection and related sequelae, and there now exist several approved formulations that protect against both high- and low-risk types. Despite the advent of vaccination, early detection and treatment of cervical and anal precancerous lesions continues to be integral to secondary prevention-molecular HPV testing, cytology, and tissue biopsy allow for triaging of patients, after which appropriate treatment with close follow-up can avert cancer development.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.
Ecological applications : a publication of the Ecological Society of America, 35(1):e70007.
As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.
Additional Links: PMID-39950593
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PubMed:
Citation:
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@article {pmid39950593,
year = {2025},
author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME},
title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {35},
number = {1},
pages = {e70007},
doi = {10.1002/eap.70007},
pmid = {39950593},
issn = {1051-0761},
support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; },
mesh = {*Soil Microbiology ; *Trees ; *Fungi/physiology ; Environmental Restoration and Remediation/methods ; Microbiota ; Conservation of Natural Resources/methods ; },
abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.},
}
MeSH Terms:
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*Soil Microbiology
*Trees
*Fungi/physiology
Environmental Restoration and Remediation/methods
Microbiota
Conservation of Natural Resources/methods
RevDate: 2025-02-14
CmpDate: 2025-02-14
Causal Associations of Gut Microbiota Species With Lymphoma: A Two-Sample Mendelian Randomization Study.
Hematological oncology, 43(2):e70046.
This study aims to focus on GM at species level, exploring the causal associations with different kinds of lymphoma to provide some information on potential intervention directions in lymphoma. Data of GM taxa were extracted from the genome-wide association study conducted by the MiBioGen and Dutch Microbiome Project (DMP), and those of lymphomas were obtained from the FinnGen consortium. Inverse variance weighted (IVW) method and Bonferroni multiple correction were utilized to assess the causal associations of GM species with different kinds of lymphoma. The effect size was expressed by odds ratios (ORs) with 95% confidence intervals (CIs). Reverse causal association analysis has also been performed. Additionally, scatter plots and leave-one-out test were conducted for sensitivity analysis. After correction, the IVW estimates suggested that elevated relative abundance of species Faecalibacterium_prausnitzii had a negatively causal association with increased odds of Hodgkin's lymphoma (HL) (OR = 0.584, 95% CI: 0.516-0.662). Relative abundance of species Gordonibacter_pamelaeae, Holdemania_filiformis, Sutterella_wadsworthensis and Coprococcus_sp_ART55_1 was negatively associated with follicular lymphoma (FL) odds, whereas that of species Bifidobacterium_catenulatum and Coprococcus_comes were positively associated with FL odds (all p < 0.05). Relative abundance of species Akkermansia_muciniphila and Coprococcus_sp_ART55_1 had a negatively causal association with non-follicular lymphoma (NFL) odds, respectively, while that of Bacteroides_uniformis had a positive one (all p < 0.05). Relative abundance of species Flavonifractor_plautii was negatively linked to diffuse large B-cell lymphoma (DLBCL) risk (OR = 0.471, 95% CI: 0.344-0.645). Relative abundance of species Eggerthella_unclassified was positively associated with T/NK cell lymphoma (TNK) risk while that of Ruminococcus_lactaris was negatively associated with TNK risk (all p < 0.05). Elevated relative abundance of Parabacteroides_unclassified was associated with higher risk of non-Hodgkin's lymphoma (NHL) (OR = 1.955, 95% CI: 1.654-2.312). The relative abundance of species Holdemania_filiformis was negatively associated with mantle cell lymphoma (MCL) risk (OR = 0.637, 95% CI: 0.544-0.746). The relative abundance of species Rothia_mucilaginosa and Lachnospiraceae_bacterium_3_1_46FAA had positively causal association with marginal zone lymphoma (MZL) risk, while that of species Alistipes_senegalensis had a negative one (all p < 0.05). This study identified 16 GM species that have potential causal associations with different kinds of lymphoma, which provided some new idea for further exploration on prevention and treatment targets in lymphoma.
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@article {pmid39950509,
year = {2025},
author = {Li, M and Wang, L and Peng, Z and Jiang, L and Yan, Y and Xia, Y and Wang, Y and Guo, L and Miao, J and Bian, Y},
title = {Causal Associations of Gut Microbiota Species With Lymphoma: A Two-Sample Mendelian Randomization Study.},
journal = {Hematological oncology},
volume = {43},
number = {2},
pages = {e70046},
doi = {10.1002/hon.70046},
pmid = {39950509},
issn = {1099-1069},
support = {82104671//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Lymphoma/epidemiology ; },
abstract = {This study aims to focus on GM at species level, exploring the causal associations with different kinds of lymphoma to provide some information on potential intervention directions in lymphoma. Data of GM taxa were extracted from the genome-wide association study conducted by the MiBioGen and Dutch Microbiome Project (DMP), and those of lymphomas were obtained from the FinnGen consortium. Inverse variance weighted (IVW) method and Bonferroni multiple correction were utilized to assess the causal associations of GM species with different kinds of lymphoma. The effect size was expressed by odds ratios (ORs) with 95% confidence intervals (CIs). Reverse causal association analysis has also been performed. Additionally, scatter plots and leave-one-out test were conducted for sensitivity analysis. After correction, the IVW estimates suggested that elevated relative abundance of species Faecalibacterium_prausnitzii had a negatively causal association with increased odds of Hodgkin's lymphoma (HL) (OR = 0.584, 95% CI: 0.516-0.662). Relative abundance of species Gordonibacter_pamelaeae, Holdemania_filiformis, Sutterella_wadsworthensis and Coprococcus_sp_ART55_1 was negatively associated with follicular lymphoma (FL) odds, whereas that of species Bifidobacterium_catenulatum and Coprococcus_comes were positively associated with FL odds (all p < 0.05). Relative abundance of species Akkermansia_muciniphila and Coprococcus_sp_ART55_1 had a negatively causal association with non-follicular lymphoma (NFL) odds, respectively, while that of Bacteroides_uniformis had a positive one (all p < 0.05). Relative abundance of species Flavonifractor_plautii was negatively linked to diffuse large B-cell lymphoma (DLBCL) risk (OR = 0.471, 95% CI: 0.344-0.645). Relative abundance of species Eggerthella_unclassified was positively associated with T/NK cell lymphoma (TNK) risk while that of Ruminococcus_lactaris was negatively associated with TNK risk (all p < 0.05). Elevated relative abundance of Parabacteroides_unclassified was associated with higher risk of non-Hodgkin's lymphoma (NHL) (OR = 1.955, 95% CI: 1.654-2.312). The relative abundance of species Holdemania_filiformis was negatively associated with mantle cell lymphoma (MCL) risk (OR = 0.637, 95% CI: 0.544-0.746). The relative abundance of species Rothia_mucilaginosa and Lachnospiraceae_bacterium_3_1_46FAA had positively causal association with marginal zone lymphoma (MZL) risk, while that of species Alistipes_senegalensis had a negative one (all p < 0.05). This study identified 16 GM species that have potential causal associations with different kinds of lymphoma, which provided some new idea for further exploration on prevention and treatment targets in lymphoma.},
}
MeSH Terms:
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Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome
Genome-Wide Association Study
Lymphoma/epidemiology
RevDate: 2025-02-14
CmpDate: 2025-02-14
Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure.
Gut microbes, 17(1):2464942.
The gut microbiome has emerged as a promising target for modulating adverse effects of opioid exposure due to its significant role in health and disease. Opioid use disorder (OUD) has become increasingly prevalent, specifically in women of reproductive age, contributing to an increased incidence of offspring exposed to opioids in utero. Recent studies have shown that prenatal opioid exposure (POE) is associated with notable changes to the maternal gut microbiome, with subsequent implications for the offspring's microbiome and other adverse outcomes. However, the role of the gut microbiome in mediating sex-based differences in pain sensitivity has not yet been investigated. In this study, both male and female C57BL/6 offspring were used to determine sex-based differences in nociception and gut microbial composition as a result of POE. Our data reveals significant sex-based differences in offspring prenatally exposed to opioids. The gut microbiome of opioid-exposed females showed an enrichment of commensal bacteria including Lactobacillus compared to opioid-exposed males. Additionally, POE females demonstrated decreased nociceptive sensitivity, while males demonstrated increased nociceptive sensitivity. RNA sequencing of the prefrontal cortex showed sex-based differences in several canonical pathways, including an increase in the opioid signaling pathway of opioid-exposed females, which was not observed in males. Microbiome modification via maternal probiotic supplementation attenuated sex-based differences throughout the early stages of life. Together, our study provides further insight on sex-based differences arising from POE and highlights the pivotal role of the gut microbiome as a modifiable target for mitigating its negative effects.
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@article {pmid39950489,
year = {2025},
author = {Singh, S and Abu, Y and Antoine, D and Gomez, D and Tao, J and Truitt, B and Roy, S},
title = {Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2464942},
doi = {10.1080/19490976.2025.2464942},
pmid = {39950489},
issn = {1949-0984},
mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; Animals ; Pregnancy ; Male ; *Dysbiosis/microbiology ; *Probiotics/administration & dosage ; Mice ; *Analgesics, Opioid/adverse effects ; *Mice, Inbred C57BL ; *Prenatal Exposure Delayed Effects/microbiology ; *Nociception/drug effects ; Bacteria/classification/isolation & purification/drug effects/genetics ; Dietary Supplements ; Sex Factors ; },
abstract = {The gut microbiome has emerged as a promising target for modulating adverse effects of opioid exposure due to its significant role in health and disease. Opioid use disorder (OUD) has become increasingly prevalent, specifically in women of reproductive age, contributing to an increased incidence of offspring exposed to opioids in utero. Recent studies have shown that prenatal opioid exposure (POE) is associated with notable changes to the maternal gut microbiome, with subsequent implications for the offspring's microbiome and other adverse outcomes. However, the role of the gut microbiome in mediating sex-based differences in pain sensitivity has not yet been investigated. In this study, both male and female C57BL/6 offspring were used to determine sex-based differences in nociception and gut microbial composition as a result of POE. Our data reveals significant sex-based differences in offspring prenatally exposed to opioids. The gut microbiome of opioid-exposed females showed an enrichment of commensal bacteria including Lactobacillus compared to opioid-exposed males. Additionally, POE females demonstrated decreased nociceptive sensitivity, while males demonstrated increased nociceptive sensitivity. RNA sequencing of the prefrontal cortex showed sex-based differences in several canonical pathways, including an increase in the opioid signaling pathway of opioid-exposed females, which was not observed in males. Microbiome modification via maternal probiotic supplementation attenuated sex-based differences throughout the early stages of life. Together, our study provides further insight on sex-based differences arising from POE and highlights the pivotal role of the gut microbiome as a modifiable target for mitigating its negative effects.},
}
MeSH Terms:
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Female
*Gastrointestinal Microbiome/drug effects
Animals
Pregnancy
Male
*Dysbiosis/microbiology
*Probiotics/administration & dosage
Mice
*Analgesics, Opioid/adverse effects
*Mice, Inbred C57BL
*Prenatal Exposure Delayed Effects/microbiology
*Nociception/drug effects
Bacteria/classification/isolation & purification/drug effects/genetics
Dietary Supplements
Sex Factors
RevDate: 2025-02-14
A Multi-Omics Meta-Analysis of Rhizosphere Microbiome Reveals Growth-Promoting Marker Bacteria at Different Stages of Legume Development.
Plant, cell & environment [Epub ahead of print].
Plant-microbe interactions have been studied extensively in legumes, but the influence of host developmental stages on its microbiome remains poorly understood. The rhizospheric region enriched with microbial diversity presents an optimal environment to investigate this relationship. We employed a multi-omics meta-analysis approach to identify the rhizospheric bacteria co-existing with legumes at different developmental stages. The data from eight different legume species across various geographical locations, soil conditions and developmental stages (vegetative, reproductive and maturation) were included in the study. A total of 10 developmental stage-specific marker bacteria were identified and found to be positively associated with plant growth phenotypes. The functional profiling elucidated the expression of these marker bacterial genes, indicating the active presence of marker bacteria. Co-expression network analysis revealed the involvement of gene clusters in biological processes such as cobalt and nitrogen metabolism. Further, pathway enrichment analysis illustrated the role of these bacteria in plant metabolic pathways, such as biosynthesis of various plant secondary metabolites, biotin metabolism and carbon fixation in photosynthetic organisms. Our study identified a positive relationship between marker bacteria and the host plant, suggesting their crucial role in legume growth and development that could further aid in crop improvement strategies.
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@article {pmid39950378,
year = {2025},
author = {Sahil, R and Pal, V and Kharat, AS and Jain, M},
title = {A Multi-Omics Meta-Analysis of Rhizosphere Microbiome Reveals Growth-Promoting Marker Bacteria at Different Stages of Legume Development.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15429},
pmid = {39950378},
issn = {1365-3040},
support = {//This study is funded by the Department of Biotechnology, Government of India, under the National Network Project scheme./ ; },
abstract = {Plant-microbe interactions have been studied extensively in legumes, but the influence of host developmental stages on its microbiome remains poorly understood. The rhizospheric region enriched with microbial diversity presents an optimal environment to investigate this relationship. We employed a multi-omics meta-analysis approach to identify the rhizospheric bacteria co-existing with legumes at different developmental stages. The data from eight different legume species across various geographical locations, soil conditions and developmental stages (vegetative, reproductive and maturation) were included in the study. A total of 10 developmental stage-specific marker bacteria were identified and found to be positively associated with plant growth phenotypes. The functional profiling elucidated the expression of these marker bacterial genes, indicating the active presence of marker bacteria. Co-expression network analysis revealed the involvement of gene clusters in biological processes such as cobalt and nitrogen metabolism. Further, pathway enrichment analysis illustrated the role of these bacteria in plant metabolic pathways, such as biosynthesis of various plant secondary metabolites, biotin metabolism and carbon fixation in photosynthetic organisms. Our study identified a positive relationship between marker bacteria and the host plant, suggesting their crucial role in legume growth and development that could further aid in crop improvement strategies.},
}
RevDate: 2025-02-14
Application of Probiotics and Postbiotics in Neurological Disorders.
Current pharmaceutical biotechnology pii:CPB-EPUB-146526 [Epub ahead of print].
Neurological illnesses encompass a broad spectrum of conditions that affect the brain, spine, and nerves, often impairing daily functioning. The global prevalence of these illnesses is rising, posing significant health challenges. This study investigates the beneficial effects of probiotics and postbiotics in managing various neurological disorders, providing a comprehensive analysis of their use in treating these conditions. The article explores innovative, holistic approaches to neurological care, emphasizing patient-centered therapeutic interventions. Compelling evidence suggests that probiotics and postbiotics positively impact several neurological diseases. Specifically, the findings indicate that these treatments can modulate the gut-brain axis, reduce neuroinflammation, and enhance neuronal protection. The study highlights the potential of specific bacteria and their byproducts to ameliorate neurological disorders. Despite promising results, the current data underscore the challenges in future research on the therapeutic benefits of probiotics and postbiotics for neurological illnesses and underscores the critical role of the gut-brain connection and the microbiome in maintaining neurological health. It also examines the safety and feasibility of using probiotics and postbiotics as adjunct therapies, delving into the mechanisms underlying their beneficial effects. Probiotics and postbiotics demonstrate a capacity to enhance the regenerative potential of the human brain, and recent evaluations provide additional evidence supporting their efficacy and safety. However, further rigorous clinical trials are necessary to validate these findings and establish the most effective therapeutic strategies for treating neurological disorders.
Additional Links: PMID-39950272
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PubMed:
Citation:
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@article {pmid39950272,
year = {2025},
author = {Mohammadpour, D and Asadollahi, A and Ozma, MA and Mehramuz, B and Ganbarov, K and Kafil, HS},
title = {Application of Probiotics and Postbiotics in Neurological Disorders.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010336767250128072101},
pmid = {39950272},
issn = {1873-4316},
abstract = {Neurological illnesses encompass a broad spectrum of conditions that affect the brain, spine, and nerves, often impairing daily functioning. The global prevalence of these illnesses is rising, posing significant health challenges. This study investigates the beneficial effects of probiotics and postbiotics in managing various neurological disorders, providing a comprehensive analysis of their use in treating these conditions. The article explores innovative, holistic approaches to neurological care, emphasizing patient-centered therapeutic interventions. Compelling evidence suggests that probiotics and postbiotics positively impact several neurological diseases. Specifically, the findings indicate that these treatments can modulate the gut-brain axis, reduce neuroinflammation, and enhance neuronal protection. The study highlights the potential of specific bacteria and their byproducts to ameliorate neurological disorders. Despite promising results, the current data underscore the challenges in future research on the therapeutic benefits of probiotics and postbiotics for neurological illnesses and underscores the critical role of the gut-brain connection and the microbiome in maintaining neurological health. It also examines the safety and feasibility of using probiotics and postbiotics as adjunct therapies, delving into the mechanisms underlying their beneficial effects. Probiotics and postbiotics demonstrate a capacity to enhance the regenerative potential of the human brain, and recent evaluations provide additional evidence supporting their efficacy and safety. However, further rigorous clinical trials are necessary to validate these findings and establish the most effective therapeutic strategies for treating neurological disorders.},
}
RevDate: 2025-02-14
Unraveling the pathogenesis of Barrett's esophagus and esophageal adenocarcinoma: the "omics" era.
Frontiers in oncology, 14:1458138.
Barrett's esophagus (BE) represents a pre-cancerous condition that is characterized by the metaplastic conversion of the squamous esophageal epithelium to a columnar intestinal-like phenotype. BE is the consequence of chronic reflux disease and has a potential progression burden to esophageal adenocarcinoma (EAC). The pathogenesis of BE and EAC has been extensively studied but not completely understood, and it is based on two main hypotheses: "transdifferentiation" and "transcommitment". Omics technologies, thanks to the potentiality of managing huge amounts of genetic and epigenetic data, sequencing the whole genome, have revolutionized the understanding of BE carcinogenesis, paving the way for biomarker development helpful in early diagnosis and risk progression assessment. Genomics and transcriptomics studies, implemented with the most advanced bioinformatics technologies, have brought to light many new risk loci and genomic alterations connected to BE and its progression to EAC, further exploring the complex pathogenesis of the disease. Early mutations of the TP53 gene, together with late aberrations of other oncosuppressor genes (SMAD4 or CKND2A), represent a genetic driving force behind BE. Genomic instability, nonetheless, is the central core of the disease. The implementation of transcriptomic and proteomic analysis, even at the single-cell level, has widened the horizons, complementing the genomic alterations with their transcriptional and translational bond. Increasing interest has been gathered around small circulating genetic traces (circulating-free DNA and micro-RNAs) with a potential role as blood biomarkers. Epigenetic alterations (such as hyper or hypo-methylation) play a meaningful role in esophageal carcinogenesis as well as the study of the tumor micro-environment, which has led to the development of novel immunological therapeutic options. Finally, the esophageal microbiome could be the protagonist to be investigated, deepening our understanding of the subtle association between the host microbiota and tumor development.
Additional Links: PMID-39950103
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Citation:
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@article {pmid39950103,
year = {2024},
author = {Barchi, A and Dell'Anna, G and Massimino, L and Mandarino, FV and Vespa, E and Viale, E and Passaretti, S and Annese, V and Malesci, A and Danese, S and Ungaro, F},
title = {Unraveling the pathogenesis of Barrett's esophagus and esophageal adenocarcinoma: the "omics" era.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1458138},
pmid = {39950103},
issn = {2234-943X},
abstract = {Barrett's esophagus (BE) represents a pre-cancerous condition that is characterized by the metaplastic conversion of the squamous esophageal epithelium to a columnar intestinal-like phenotype. BE is the consequence of chronic reflux disease and has a potential progression burden to esophageal adenocarcinoma (EAC). The pathogenesis of BE and EAC has been extensively studied but not completely understood, and it is based on two main hypotheses: "transdifferentiation" and "transcommitment". Omics technologies, thanks to the potentiality of managing huge amounts of genetic and epigenetic data, sequencing the whole genome, have revolutionized the understanding of BE carcinogenesis, paving the way for biomarker development helpful in early diagnosis and risk progression assessment. Genomics and transcriptomics studies, implemented with the most advanced bioinformatics technologies, have brought to light many new risk loci and genomic alterations connected to BE and its progression to EAC, further exploring the complex pathogenesis of the disease. Early mutations of the TP53 gene, together with late aberrations of other oncosuppressor genes (SMAD4 or CKND2A), represent a genetic driving force behind BE. Genomic instability, nonetheless, is the central core of the disease. The implementation of transcriptomic and proteomic analysis, even at the single-cell level, has widened the horizons, complementing the genomic alterations with their transcriptional and translational bond. Increasing interest has been gathered around small circulating genetic traces (circulating-free DNA and micro-RNAs) with a potential role as blood biomarkers. Epigenetic alterations (such as hyper or hypo-methylation) play a meaningful role in esophageal carcinogenesis as well as the study of the tumor micro-environment, which has led to the development of novel immunological therapeutic options. Finally, the esophageal microbiome could be the protagonist to be investigated, deepening our understanding of the subtle association between the host microbiota and tumor development.},
}
RevDate: 2025-02-14
Mixtures of logistic normal multinomial regression models for microbiome data.
Journal of applied statistics, 52(3):624-655.
In the realm of bioinformatics, we frequently encounter discrete data, particularly microbiome taxa count data obtained through 16S rRNA sequencing. These microbiome datasets are commonly characterized by their high dimensionality and the ability to provide insights solely into relative abundance, necessitating their classification as compositional data. Analyzing such data presents challenges due to their confinement within a simplex. Additionally, microbiome taxa counts are subject to influence by various biological and environmental factors like age, gender, and diet. Thus, we have developed a novel approach involving regression-based mixtures of logistic normal multinomial models for clustering microbiome data. These models effectively categorize samples into more homogeneous subpopulations, enabling the exploration of relationships between bacterial abundance and biological or environmental covariates within each identified group. To enhance the accuracy and efficiency of parameter estimation, we employ a robust framework based on variational Gaussian approximations (VGA). Our proposed method's effectiveness is demonstrated through its application to simulated and real datasets.
Additional Links: PMID-39950023
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Citation:
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@article {pmid39950023,
year = {2025},
author = {Dai, W and Fang, Y and Subedi, S},
title = {Mixtures of logistic normal multinomial regression models for microbiome data.},
journal = {Journal of applied statistics},
volume = {52},
number = {3},
pages = {624-655},
pmid = {39950023},
issn = {0266-4763},
abstract = {In the realm of bioinformatics, we frequently encounter discrete data, particularly microbiome taxa count data obtained through 16S rRNA sequencing. These microbiome datasets are commonly characterized by their high dimensionality and the ability to provide insights solely into relative abundance, necessitating their classification as compositional data. Analyzing such data presents challenges due to their confinement within a simplex. Additionally, microbiome taxa counts are subject to influence by various biological and environmental factors like age, gender, and diet. Thus, we have developed a novel approach involving regression-based mixtures of logistic normal multinomial models for clustering microbiome data. These models effectively categorize samples into more homogeneous subpopulations, enabling the exploration of relationships between bacterial abundance and biological or environmental covariates within each identified group. To enhance the accuracy and efficiency of parameter estimation, we employ a robust framework based on variational Gaussian approximations (VGA). Our proposed method's effectiveness is demonstrated through its application to simulated and real datasets.},
}
RevDate: 2025-02-14
Implications of type 1 diabetes mellitus in the etiology and clinic of dento-maxillary anomalies - questionnaire-based evaluation of the dentists' opinion.
Medicine and pharmacy reports, 98(1):135-143.
BACKGROUND AND AIMS: Type 1 diabetes is one of the most common chronic childhood diseases, which can be diagnosed at any age, with implications on the general development, but also on the craniofacial structure. It is widely speculated that diabetes occurs when inherited genetic characteristics are triggered by environmental factors. Oral pathology is complex and it includes a series of clinical entities: dental caries, periodontal disease, dento-maxillary anomalies, diseases of the oral mucosa, which implies a significant responsibility for the doctor, but also for society. This study aims to highlight the association of dento-maxillary anomalies with juvenile diabetes, starting from its increased prevalence among children and adolescents, the oral manifestations of diabetes mellitus and its influence on the oral microbiome, the increased incidence of periodontal and dental diseases, by means of a questionnaire.
METHOD: A cross-sectional study was carried out on a number of 60 dentists, between 01.01.2023 and 01.03.2024, using a questionnaire with 14 items, which was distributed by e-mail and social networks to dentists of different specialties, from various university. Before completing the questionnaire, the doctors were informed about the purpose of the study and that their answers were anonymous and did not imply any responsibility.
RESULTS: Our results indicated awareness of the association between oral health, the presence of dento-maxillary anomalies and the pathology of type 1 diabetes, among dentists of different specialties. The most frequent changes that occur in the oral cavity in the examined patients are represented by carious lesions, reported by 21 examiners (35.00%), of which 18 (39.13%) are female, aged between 25-35 years.Among the reported dentomaxillary anomalies, those of Angle class II were the most frequent - 17 examiners (28.33%), of which 12 (26.09%) are female reported the presence of these anomalies. The presence of Angle class I anomalies was reported by 13 examiners (21.67%) of which 9 (19.57%) are female, while 6 examiners (10.00%) reported the presence of Angle class III anomalies.
CONCLUSIONS: The evaluation of modern therapeutic methods through questionnaires distributed online represents a feedback of the tested activity and shows that most doctors know the correlations between diabetes and oro-dental diseases and have an obvious healthy attitude. The possible association between oral diseases and the presence of type 1 diabetes was reported by most of the dentists interviewed, however the information on the correlations between oral health and the presence of type 1 diabetes in children was not sufficiently explored by dentists. The dentist must know the clinical particularities of diabetes mellitus and its implications on the oral status, in order to be able to intervene effectively in reducing the oral and systemic complications of diabetes.
Additional Links: PMID-39949908
PubMed:
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@article {pmid39949908,
year = {2025},
author = {Dămăşaru, MS and Păcurar, M and Mariş, M and Dămăşaru, E and Mariş, M and Tilinca, CM},
title = {Implications of type 1 diabetes mellitus in the etiology and clinic of dento-maxillary anomalies - questionnaire-based evaluation of the dentists' opinion.},
journal = {Medicine and pharmacy reports},
volume = {98},
number = {1},
pages = {135-143},
pmid = {39949908},
issn = {2668-0572},
abstract = {BACKGROUND AND AIMS: Type 1 diabetes is one of the most common chronic childhood diseases, which can be diagnosed at any age, with implications on the general development, but also on the craniofacial structure. It is widely speculated that diabetes occurs when inherited genetic characteristics are triggered by environmental factors. Oral pathology is complex and it includes a series of clinical entities: dental caries, periodontal disease, dento-maxillary anomalies, diseases of the oral mucosa, which implies a significant responsibility for the doctor, but also for society. This study aims to highlight the association of dento-maxillary anomalies with juvenile diabetes, starting from its increased prevalence among children and adolescents, the oral manifestations of diabetes mellitus and its influence on the oral microbiome, the increased incidence of periodontal and dental diseases, by means of a questionnaire.
METHOD: A cross-sectional study was carried out on a number of 60 dentists, between 01.01.2023 and 01.03.2024, using a questionnaire with 14 items, which was distributed by e-mail and social networks to dentists of different specialties, from various university. Before completing the questionnaire, the doctors were informed about the purpose of the study and that their answers were anonymous and did not imply any responsibility.
RESULTS: Our results indicated awareness of the association between oral health, the presence of dento-maxillary anomalies and the pathology of type 1 diabetes, among dentists of different specialties. The most frequent changes that occur in the oral cavity in the examined patients are represented by carious lesions, reported by 21 examiners (35.00%), of which 18 (39.13%) are female, aged between 25-35 years.Among the reported dentomaxillary anomalies, those of Angle class II were the most frequent - 17 examiners (28.33%), of which 12 (26.09%) are female reported the presence of these anomalies. The presence of Angle class I anomalies was reported by 13 examiners (21.67%) of which 9 (19.57%) are female, while 6 examiners (10.00%) reported the presence of Angle class III anomalies.
CONCLUSIONS: The evaluation of modern therapeutic methods through questionnaires distributed online represents a feedback of the tested activity and shows that most doctors know the correlations between diabetes and oro-dental diseases and have an obvious healthy attitude. The possible association between oral diseases and the presence of type 1 diabetes was reported by most of the dentists interviewed, however the information on the correlations between oral health and the presence of type 1 diabetes in children was not sufficiently explored by dentists. The dentist must know the clinical particularities of diabetes mellitus and its implications on the oral status, in order to be able to intervene effectively in reducing the oral and systemic complications of diabetes.},
}
RevDate: 2025-02-14
The association between exocrine pancreatic insufficiency and changes in gut microbiota: a narrative review.
Medicine and pharmacy reports, 98(1):5-12.
Due to their physical proximity, the healthy pancreas and the gut microbiome are known to interact in a variety of ways. The gut microbiota has been recognized as a potential factor in the development and progression of exocrine pancreatic insufficiency through several mechanisms. Pancreatic diseases like chronic and acute pancreatitis or pancreatic cancer are frequently accompanied by pancreatic exocrine insufficiency which affects the gut microbiota. Firstly, the gut microbes are controlled by antimicrobial pancreatic secretions, while themselves induce the secretion of substances by the pancreas through metabolite production, such as short-chain fatty acids. Secondly, dysbiosis, the alteration in the abundance and diversity of different species, has been observed in patients with pancreatic diseases. Dysbiosis influences carcinogenesis in pancreatic cancer in ways that are either procarcinogenic or anticarcinogenic and finding these connections will have clinical implications. Identifying microbial biomarkers allow for an earlier diagnosis, improved therapy and prognosis in pancreatic cancer. The gut microbiome has a role in the pathogenesis of pancreatitis by either a bacterial translocation or a host immune response mechanism. The disruption of the normal gut barrier is believed to be the primary source of bacteria in acute pancreatitis which leads to infected pancreatic necrosis. In this paper, we review the current data about the association between pancreatic diseases linked to exocrine insufficiency and gut microbiota.
Additional Links: PMID-39949904
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@article {pmid39949904,
year = {2025},
author = {Şeulean, EC and Dumitraşcu, DL},
title = {The association between exocrine pancreatic insufficiency and changes in gut microbiota: a narrative review.},
journal = {Medicine and pharmacy reports},
volume = {98},
number = {1},
pages = {5-12},
pmid = {39949904},
issn = {2668-0572},
abstract = {Due to their physical proximity, the healthy pancreas and the gut microbiome are known to interact in a variety of ways. The gut microbiota has been recognized as a potential factor in the development and progression of exocrine pancreatic insufficiency through several mechanisms. Pancreatic diseases like chronic and acute pancreatitis or pancreatic cancer are frequently accompanied by pancreatic exocrine insufficiency which affects the gut microbiota. Firstly, the gut microbes are controlled by antimicrobial pancreatic secretions, while themselves induce the secretion of substances by the pancreas through metabolite production, such as short-chain fatty acids. Secondly, dysbiosis, the alteration in the abundance and diversity of different species, has been observed in patients with pancreatic diseases. Dysbiosis influences carcinogenesis in pancreatic cancer in ways that are either procarcinogenic or anticarcinogenic and finding these connections will have clinical implications. Identifying microbial biomarkers allow for an earlier diagnosis, improved therapy and prognosis in pancreatic cancer. The gut microbiome has a role in the pathogenesis of pancreatitis by either a bacterial translocation or a host immune response mechanism. The disruption of the normal gut barrier is believed to be the primary source of bacteria in acute pancreatitis which leads to infected pancreatic necrosis. In this paper, we review the current data about the association between pancreatic diseases linked to exocrine insufficiency and gut microbiota.},
}
RevDate: 2025-02-14
Editorial: Host-diet-microbiome interactions in obesity prevention and treatment.
Frontiers in nutrition, 11:1541977.
Additional Links: PMID-39949868
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@article {pmid39949868,
year = {2024},
author = {Barouei, J and Kable, ME and Moussavi, M and Hsieh, YH},
title = {Editorial: Host-diet-microbiome interactions in obesity prevention and treatment.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1541977},
doi = {10.3389/fnut.2024.1541977},
pmid = {39949868},
issn = {2296-861X},
}
RevDate: 2025-02-14
Assembly and network of Rhei Radix et Rhizoma surface microbiome shaped by processing methods and sampling locations.
Chinese herbal medicines, 17(1):189-199.
OBJECTIVE: Rhei Radix et Rhizoma has five types of products, namely, raw rhubarb (RR), wine rhubarb (WR), vinegar rhubarb (VR), cooked rhubarb (CR), and rhubarb charcoal (RC). However, Rhei Radix et Rhizoma is easily contaminated with fungi and mycotoxins if not harvested or processed properly. Here, we intend to analyze how microbiome assemblies and co-occurrence patterns are influenced by sampling locations and processing methods.
METHODS: High-throughput sequencing and internal transcribed spacer 2 (ITS2) were carried out to study the diversities (α- and β-diversity), composition (dominant taxa and potential biomarkers), and network complexitity of surface fungi on RR, WR, VR, CR, and RC collected from Gansu and Sichuan provinces, China.
RESULTS: The phyla Ascomycota and Basidiomycota; the genera Kazachstania, Malassezia, and Asterotremella; and the species Kazachstania exigua, Asterotremella pseudolonga, and Malassezia restricta were the dominant fungi and exhibited differences in the two provinces and the five processed products. The α-diversity and network complexity were strongly dependent on processing methods. Chao 1, the Shannon index, and network complexity and connectivity were highest in the CR group. The α-diversity and network complexity were influenced by sampling locations. Chao 1 and network complexity and connectivity were highest in the Gansu Province.
CONCLUSION: The assembly and network of the surface microbiome on Rhei Radix et Rhizoma were shaped by processing methods and sampling locations. This paper offers a comprehensive understanding of microorganisms, which can provide early warning for potential mycotoxins and ensure the safety of drugs and consumers.
Additional Links: PMID-39949799
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@article {pmid39949799,
year = {2025},
author = {Wei, G and Chen, X and Zhang, G and Liang, C and Zhang, Z and Zhang, B and Chen, S and Dong, L},
title = {Assembly and network of Rhei Radix et Rhizoma surface microbiome shaped by processing methods and sampling locations.},
journal = {Chinese herbal medicines},
volume = {17},
number = {1},
pages = {189-199},
pmid = {39949799},
issn = {2589-3610},
abstract = {OBJECTIVE: Rhei Radix et Rhizoma has five types of products, namely, raw rhubarb (RR), wine rhubarb (WR), vinegar rhubarb (VR), cooked rhubarb (CR), and rhubarb charcoal (RC). However, Rhei Radix et Rhizoma is easily contaminated with fungi and mycotoxins if not harvested or processed properly. Here, we intend to analyze how microbiome assemblies and co-occurrence patterns are influenced by sampling locations and processing methods.
METHODS: High-throughput sequencing and internal transcribed spacer 2 (ITS2) were carried out to study the diversities (α- and β-diversity), composition (dominant taxa and potential biomarkers), and network complexitity of surface fungi on RR, WR, VR, CR, and RC collected from Gansu and Sichuan provinces, China.
RESULTS: The phyla Ascomycota and Basidiomycota; the genera Kazachstania, Malassezia, and Asterotremella; and the species Kazachstania exigua, Asterotremella pseudolonga, and Malassezia restricta were the dominant fungi and exhibited differences in the two provinces and the five processed products. The α-diversity and network complexity were strongly dependent on processing methods. Chao 1, the Shannon index, and network complexity and connectivity were highest in the CR group. The α-diversity and network complexity were influenced by sampling locations. Chao 1 and network complexity and connectivity were highest in the Gansu Province.
CONCLUSION: The assembly and network of the surface microbiome on Rhei Radix et Rhizoma were shaped by processing methods and sampling locations. This paper offers a comprehensive understanding of microorganisms, which can provide early warning for potential mycotoxins and ensure the safety of drugs and consumers.},
}
RevDate: 2025-02-14
Detection of porphyromonas gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma using qRT-PCR: A comparative study.
Journal of oral and maxillofacial pathology : JOMFP, 28(4):583-588.
BACKGROUND: Recent researches has shown a significant association between microorganisms and oral squamous cell carcinoma (OSCC). Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis, is considered as an important potential etiologic agent of OSCC, but the underlying mechanisms by which P. gingivalis mediates OSCC progression remain poorly understood.
AIM: The aim of this study was to compare the levels of P. gingivalis in oral potentially malignant disorders, oral squamous cell carcinoma and normal oral mucosa using qRT-PCR.
METHOD AND MATERIAL: Genomic DNA was extracted and quantified, and the expression of the P. gingivalis levels was done in 16 cases of oral potentially malignant disorders, 16 cases of oral squamous cell carcinoma and 16 cases of normal oral mucosa by quantitative real-time polymerase chain reaction (RT-qPCR).
RESULTS: It was observed that there was an over expression of P. gingivalis in both oral potentially malignant disorders and oral squamous cell carcinoma with good mean cycle threshold (CT) value of 27.00 and 27.55, respectively. When comparing the levels of P. gingivalis in three groups, oral potentially malignant disorders (OPMD) and oral squamous cell carcinoma (OSCC) showed higher expression than normal mucosa and in between two groups OSCC showed higher expression than OPMD and the difference is statistically significant with P value less than 0.001.
CONCLUSION: Our findings suggest that there is an over expression of P. gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma, compared to normal mucosa and highly expressed in OSCCs compared to OPMD. Increased levels of P. gingivalis in OPMDs and OSCCs may suggest the early event of tumorigenesis. Hence, it can be used as a valuable marker for early diagnosis, prognosis marker and in the identification of therapeutic targets.
Additional Links: PMID-39949692
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@article {pmid39949692,
year = {2024},
author = {Suganya, G and Sahana, NS and Akalya, P and Yadav, ST and Suresh, T and Chandrakala, J},
title = {Detection of porphyromonas gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma using qRT-PCR: A comparative study.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {28},
number = {4},
pages = {583-588},
pmid = {39949692},
issn = {0973-029X},
abstract = {BACKGROUND: Recent researches has shown a significant association between microorganisms and oral squamous cell carcinoma (OSCC). Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis, is considered as an important potential etiologic agent of OSCC, but the underlying mechanisms by which P. gingivalis mediates OSCC progression remain poorly understood.
AIM: The aim of this study was to compare the levels of P. gingivalis in oral potentially malignant disorders, oral squamous cell carcinoma and normal oral mucosa using qRT-PCR.
METHOD AND MATERIAL: Genomic DNA was extracted and quantified, and the expression of the P. gingivalis levels was done in 16 cases of oral potentially malignant disorders, 16 cases of oral squamous cell carcinoma and 16 cases of normal oral mucosa by quantitative real-time polymerase chain reaction (RT-qPCR).
RESULTS: It was observed that there was an over expression of P. gingivalis in both oral potentially malignant disorders and oral squamous cell carcinoma with good mean cycle threshold (CT) value of 27.00 and 27.55, respectively. When comparing the levels of P. gingivalis in three groups, oral potentially malignant disorders (OPMD) and oral squamous cell carcinoma (OSCC) showed higher expression than normal mucosa and in between two groups OSCC showed higher expression than OPMD and the difference is statistically significant with P value less than 0.001.
CONCLUSION: Our findings suggest that there is an over expression of P. gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma, compared to normal mucosa and highly expressed in OSCCs compared to OPMD. Increased levels of P. gingivalis in OPMDs and OSCCs may suggest the early event of tumorigenesis. Hence, it can be used as a valuable marker for early diagnosis, prognosis marker and in the identification of therapeutic targets.},
}
RevDate: 2025-02-14
The oral-lung microbiome dysbiosis: Unravelling its role in implications for chronic obstructive pulmonary disease (COPD) pathogenesis.
Journal of oral and maxillofacial pathology : JOMFP, 28(4):619-625.
BACKGROUND: The impact of the oral flora on the composition of the microbiome in the lungs is substantial in both healthy and diseased conditions, contributing significantly to its intricacy. There is mounting evidence from microbiological research that suggests a major ecological relationship between periodontitis, Chronic Obstructive Pulmonary Disease (COPD), and oral microecosystems. An association has been established between respiratory diseases and disruptions in the symbiotic equilibrium of the oral microbiome. This study aims to explore the intricate connections between oral health and lung microflora, particularly about the pathogenesis of COPD, and to highlight the implications for future research and clinical practice.
MATERIALS AND METHODS: Subgingival Plaque samples were collected from a total of 120 participants with 30 healthy Control (H group),30 Periodontitis with no COPD (P group), 30 COPD with periodontally healthy (COPD) and 30 individuals with COPD and Periodontitis (COPD+ P). All participants underwent evaluation of periodontal measurements like Pocket Depth (PD), Clinical loss of Attachment (CAL), Gingival Index (GI), and Plaque Index (PI) Bacterial DNA was extracted and quantified using Real-time polymerase chain reaction. Using the One-dimensional Analysis of Variance (ANOVA) and post-analysis test for multiple comparisons, the mean values of all the clinical parameters were analyzed among the four participant groups. Using the Pearson Correlation coefficient, the parameters were correlated.
RESULTS: Statistical relevant relation was shown among Probing Depth (PD), Clinical Loss of Attachment (CAL), Plaque Index (PI) and Gingival Index (GI) in the COPD+P group. Increased prevalence of Pa (Pseudomonas aeroginosa) seen among P group and COPD+P. A substantial inverse relationship was seen between the absolute levels of Pa, CAL, PI, and lung function measures (Fev1, Fev1/FVC).
CONCLUSION: The importance of maintaining dental health in the prevention and treatment of respiratory disorders is highlighted by the relationships that exist between the oral microecosystem, oral hygiene, and respiratory pathologies. There is substantial potential to decrease the occurrence of respiratory illnesses by practicing good oral care and strategically managing the balance of the oral microbial flora. Therefore, future research efforts should prioritize the characterization of the precise impact of the oral microbiota on pulmonary health and use this knowledge towards developing innovative preventive and treatment measures targeted at combating respiratory infections and related diseases.
Additional Links: PMID-39949674
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@article {pmid39949674,
year = {2024},
author = {Mithradas, N and Sudhakar, U and Shanmugapriya, K and Jeddy, N and Ram, S},
title = {The oral-lung microbiome dysbiosis: Unravelling its role in implications for chronic obstructive pulmonary disease (COPD) pathogenesis.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {28},
number = {4},
pages = {619-625},
pmid = {39949674},
issn = {0973-029X},
abstract = {BACKGROUND: The impact of the oral flora on the composition of the microbiome in the lungs is substantial in both healthy and diseased conditions, contributing significantly to its intricacy. There is mounting evidence from microbiological research that suggests a major ecological relationship between periodontitis, Chronic Obstructive Pulmonary Disease (COPD), and oral microecosystems. An association has been established between respiratory diseases and disruptions in the symbiotic equilibrium of the oral microbiome. This study aims to explore the intricate connections between oral health and lung microflora, particularly about the pathogenesis of COPD, and to highlight the implications for future research and clinical practice.
MATERIALS AND METHODS: Subgingival Plaque samples were collected from a total of 120 participants with 30 healthy Control (H group),30 Periodontitis with no COPD (P group), 30 COPD with periodontally healthy (COPD) and 30 individuals with COPD and Periodontitis (COPD+ P). All participants underwent evaluation of periodontal measurements like Pocket Depth (PD), Clinical loss of Attachment (CAL), Gingival Index (GI), and Plaque Index (PI) Bacterial DNA was extracted and quantified using Real-time polymerase chain reaction. Using the One-dimensional Analysis of Variance (ANOVA) and post-analysis test for multiple comparisons, the mean values of all the clinical parameters were analyzed among the four participant groups. Using the Pearson Correlation coefficient, the parameters were correlated.
RESULTS: Statistical relevant relation was shown among Probing Depth (PD), Clinical Loss of Attachment (CAL), Plaque Index (PI) and Gingival Index (GI) in the COPD+P group. Increased prevalence of Pa (Pseudomonas aeroginosa) seen among P group and COPD+P. A substantial inverse relationship was seen between the absolute levels of Pa, CAL, PI, and lung function measures (Fev1, Fev1/FVC).
CONCLUSION: The importance of maintaining dental health in the prevention and treatment of respiratory disorders is highlighted by the relationships that exist between the oral microecosystem, oral hygiene, and respiratory pathologies. There is substantial potential to decrease the occurrence of respiratory illnesses by practicing good oral care and strategically managing the balance of the oral microbial flora. Therefore, future research efforts should prioritize the characterization of the precise impact of the oral microbiota on pulmonary health and use this knowledge towards developing innovative preventive and treatment measures targeted at combating respiratory infections and related diseases.},
}
RevDate: 2025-02-14
The gut microbiota regulates diabetic retinopathy in adult rats.
Frontiers in microbiology, 16:1479792.
INTRODUCTION: Diabetic retinopathy (DR) is the most common complication of diabetes. Neuronal apoptosis, activated microglia, and microvascular changes are early features of DR. The gut microbiota is critical for the maturation and activation of microglia in the brain, and DR patients exhibit gut dysbiosis. However, the effect of the gut microbiota on retinal microglia under normal or diabetic conditions is still unclear.
METHODS: Type 2 diabetes (T2D) was established in male adult Brown Norway (BN) rats, and they were treated with gavage of broad-spectrum antibiotic (ABX) suspension. Retinal fundus fluorescein angiography was performed to observe the dynamic growth process and leakage of blood vessels. Retro-orbital injection of FITC-Dextran was performed to observe the changes in blood-retinal barriers. After treatment with ABX and diabetes lasting for more than 6 months, 16S RNA sequencing of stool samples was performed to determine changes in the gut microbiome and mass spectrometry was used to analyze metabolome changes. IBA1, IB4, and Brn3 staining were performed on adult rats' retinal wholemount or sections to observe the changes in microglia, blood vessels and the number of ganglion cells.
RESULTS: Long-term (6 months) T2D caused gut dysbiosis with increased average taxa numbers. We showed that broad-spectrum antibiotics (ABXs) gavage can reduce the average number of gut microbiota taxa and retinal microglia in adult male BN rats with or without T2D. Interestingly, adult male BN rats with T2D for more than 6 months showed a loss of retinal ganglion cells (RGCs) without significant changes in retinal microglia or retinal vascular vessels. However, ABX gavage reduced retinal microglia and alleviated RGC damage in these T2D rats.
CONCLUSION: Our data suggests that ABX gavage-induced gut dysbiosis can reduce retinal microglia in adult rats and alleviate RGC loss in long-term T2D rats. Targeting the gut microbiota may be a future therapeutic strategy for DR management.
Additional Links: PMID-39949626
PubMed:
Citation:
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@article {pmid39949626,
year = {2025},
author = {Hou, J and Lv, Z and Wang, Y and Chen, D},
title = {The gut microbiota regulates diabetic retinopathy in adult rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1479792},
pmid = {39949626},
issn = {1664-302X},
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is the most common complication of diabetes. Neuronal apoptosis, activated microglia, and microvascular changes are early features of DR. The gut microbiota is critical for the maturation and activation of microglia in the brain, and DR patients exhibit gut dysbiosis. However, the effect of the gut microbiota on retinal microglia under normal or diabetic conditions is still unclear.
METHODS: Type 2 diabetes (T2D) was established in male adult Brown Norway (BN) rats, and they were treated with gavage of broad-spectrum antibiotic (ABX) suspension. Retinal fundus fluorescein angiography was performed to observe the dynamic growth process and leakage of blood vessels. Retro-orbital injection of FITC-Dextran was performed to observe the changes in blood-retinal barriers. After treatment with ABX and diabetes lasting for more than 6 months, 16S RNA sequencing of stool samples was performed to determine changes in the gut microbiome and mass spectrometry was used to analyze metabolome changes. IBA1, IB4, and Brn3 staining were performed on adult rats' retinal wholemount or sections to observe the changes in microglia, blood vessels and the number of ganglion cells.
RESULTS: Long-term (6 months) T2D caused gut dysbiosis with increased average taxa numbers. We showed that broad-spectrum antibiotics (ABXs) gavage can reduce the average number of gut microbiota taxa and retinal microglia in adult male BN rats with or without T2D. Interestingly, adult male BN rats with T2D for more than 6 months showed a loss of retinal ganglion cells (RGCs) without significant changes in retinal microglia or retinal vascular vessels. However, ABX gavage reduced retinal microglia and alleviated RGC damage in these T2D rats.
CONCLUSION: Our data suggests that ABX gavage-induced gut dysbiosis can reduce retinal microglia in adult rats and alleviate RGC loss in long-term T2D rats. Targeting the gut microbiota may be a future therapeutic strategy for DR management.},
}
RevDate: 2025-02-14
Polygonatum kingianum polysaccharide alleviated intestinal injuries by mediating antioxidant ability and microbiota.
Frontiers in microbiology, 16:1492710.
INTRODUCTION: Polygonatum kingianum is a well-known medicinal herb with proven bioactivities; however, little is known about the effects of its polysaccharide on intestinal injuries in animals induced by lipopolysaccharide (LPS).
METHODS: A total of 30 Institute of Cancer Research (ICR) mice were divided into control (CH), induced (MH), and treated (H) groups. Mice in group H were supplemented with 100 mg/kg Polygonatum kingianum polysaccharides, while groups C and M were treated with the same amount of normal saline by gavage for 18 days. On the 18[th] day animals in groups M and H were induced by LPS (10 mg/kg).
RESULTS: The results showed the weight of mice in group MH significantly dropped (P < 0.0001), while mice in the PK group had a higher weight (P < 0.01). Pathological analysis found that the majority of the villi in mice induced by LPS were broken and short, while PK-treated animals had longer and considerably integrated villi. The villi length in groups CH (P < 0.0001) and H (P < 0.0001) was longer than that in group M, and the value of villi length/crypt depth in group MH was smaller than that in groups CH (P < 0.0001) and H (P < 0.0001), while the crypt depth in group MH was higher than in groups CH (P < 0.0001) and H (P < 0.0001). Serum inspection showed that MAD (P < 0.05), IL-1β (P < 0.05), IL-6 (P < 0.05), and TNF-α (P < 0.01) were significantly higher in group MH, while SOD (P < 0.001), T-AOC (P < 0.01), and GSH-Px (P < 0.01) were notably higher in groups CH and H. Microbiome sequencing of mice obtained 844,477 raw and 725,469 filtered reads. There were 2,407 ASVs detected in animals, and there were 312 and 328 shared ASVs between CH and MH, and CH and H, respectively. There were 5 phyla and 20genera of remarkable bacteria found among mice groups including genera of Escherichia, Pseudomonas_E, Mailhella, Paramuribaculum, NM07-P-09, Odoribacter, Nanosyncoccus, SFM01, Onthenecus, Clostridium_Q, UBA6985, Ructibacterium, UBA946, Lachnoclostridium_B, Evtepia, CAG-269, Limivicinus, Formimonas, Dehalobacterium, Dwaynesavagella, and UBA6985. We revealed that Polygonatum kingianum polysaccharide could alleviate intestinal injuries by promoting oxidation resistance, decreasing inflammatory responses, and accommodating the intestinal microbiota of mice.
DISCUSSION: Our results suggest the possibility of developing novel therapies for intestinal diseases.
Additional Links: PMID-39949622
PubMed:
Citation:
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@article {pmid39949622,
year = {2025},
author = {Qiu, R and Pan, C and Qin, Y and Wei, Q and Yu, Y and Zhang, Y and Xie, X and Li, J and Chen, S and Li, K and Fouad, D and Wu, Y and Zhong, Q},
title = {Polygonatum kingianum polysaccharide alleviated intestinal injuries by mediating antioxidant ability and microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1492710},
pmid = {39949622},
issn = {1664-302X},
abstract = {INTRODUCTION: Polygonatum kingianum is a well-known medicinal herb with proven bioactivities; however, little is known about the effects of its polysaccharide on intestinal injuries in animals induced by lipopolysaccharide (LPS).
METHODS: A total of 30 Institute of Cancer Research (ICR) mice were divided into control (CH), induced (MH), and treated (H) groups. Mice in group H were supplemented with 100 mg/kg Polygonatum kingianum polysaccharides, while groups C and M were treated with the same amount of normal saline by gavage for 18 days. On the 18[th] day animals in groups M and H were induced by LPS (10 mg/kg).
RESULTS: The results showed the weight of mice in group MH significantly dropped (P < 0.0001), while mice in the PK group had a higher weight (P < 0.01). Pathological analysis found that the majority of the villi in mice induced by LPS were broken and short, while PK-treated animals had longer and considerably integrated villi. The villi length in groups CH (P < 0.0001) and H (P < 0.0001) was longer than that in group M, and the value of villi length/crypt depth in group MH was smaller than that in groups CH (P < 0.0001) and H (P < 0.0001), while the crypt depth in group MH was higher than in groups CH (P < 0.0001) and H (P < 0.0001). Serum inspection showed that MAD (P < 0.05), IL-1β (P < 0.05), IL-6 (P < 0.05), and TNF-α (P < 0.01) were significantly higher in group MH, while SOD (P < 0.001), T-AOC (P < 0.01), and GSH-Px (P < 0.01) were notably higher in groups CH and H. Microbiome sequencing of mice obtained 844,477 raw and 725,469 filtered reads. There were 2,407 ASVs detected in animals, and there were 312 and 328 shared ASVs between CH and MH, and CH and H, respectively. There were 5 phyla and 20genera of remarkable bacteria found among mice groups including genera of Escherichia, Pseudomonas_E, Mailhella, Paramuribaculum, NM07-P-09, Odoribacter, Nanosyncoccus, SFM01, Onthenecus, Clostridium_Q, UBA6985, Ructibacterium, UBA946, Lachnoclostridium_B, Evtepia, CAG-269, Limivicinus, Formimonas, Dehalobacterium, Dwaynesavagella, and UBA6985. We revealed that Polygonatum kingianum polysaccharide could alleviate intestinal injuries by promoting oxidation resistance, decreasing inflammatory responses, and accommodating the intestinal microbiota of mice.
DISCUSSION: Our results suggest the possibility of developing novel therapies for intestinal diseases.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Characterization of serum metabolome and respiratory microbiota in children with influenza A virus infection.
Frontiers in cellular and infection microbiology, 14:1478876.
The risk of children being infected with Influenza A virus (IAV) is high, and if not treated promptly, it can lead to serious illness. Compared with control group, IAV infection decreased the contents of platelet, white blood cell, lymphocyte, eosinophil, basophil, CD3[+] T cells, CD4[+] T cells, CD8[+] T cells, and B cells, while increasing the number of red blood cell. Additionally, IAV infection increased serum concentrations of total protein, albumin and lipase, while decreasing the contents of calcium, triglyceride, total bilirubin, direct bilirubin, indirect bilirubin and gamma-glutamyltransferase. However, the interactions between the respiratory microbiome and metabolites and their impact on IAV in children remains unclear. Ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) and 16S rRNA gene sequencing were employed to analysis the respiratory microbiome and serum metabolic characteristics of 85 patients with IAV infection and age-matched 55 controls with respiratory disease who tested negative for 13 types of respiratory pathogens. The serum metabolic profile of IAV patients was significantly changed, and the purine metabolism was destroyed. Purine metabolism was also enriched in H3N2 patients compared to H1N1, with increased xanthine, deoxyguanosine, and inosine. The respiratory microbiome structure in children with IAV, including H1N1 and H3N2, was significantly different from that of the control, with significantly increased Chao index. The Mantel test revealed the correlation and consistency in the trends of Haemophilus, Ureaplasma and Inosine. This study revealed the characteristics of the respiratory microbiome and serum metabolites in pediatric patients with IAV, providing a new direction for exploring the pathogenesis of IAV in children.
Additional Links: PMID-39949573
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Citation:
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@article {pmid39949573,
year = {2024},
author = {Shi, X and Hua, S and Chen, Z and Cao, W and Xiao, M and Pei, W and Cao, Z and Zhang, Z and Yang, H and Shao, X and Xia, Y},
title = {Characterization of serum metabolome and respiratory microbiota in children with influenza A virus infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1478876},
pmid = {39949573},
issn = {2235-2988},
mesh = {Humans ; *Influenza, Human/blood ; *Metabolome ; *Microbiota ; Female ; Male ; Child, Preschool ; Child ; RNA, Ribosomal, 16S/genetics ; Influenza A virus ; Infant ; Influenza A Virus, H1N1 Subtype ; Influenza A Virus, H3N2 Subtype ; Serum/chemistry ; Adolescent ; Mass Spectrometry ; },
abstract = {The risk of children being infected with Influenza A virus (IAV) is high, and if not treated promptly, it can lead to serious illness. Compared with control group, IAV infection decreased the contents of platelet, white blood cell, lymphocyte, eosinophil, basophil, CD3[+] T cells, CD4[+] T cells, CD8[+] T cells, and B cells, while increasing the number of red blood cell. Additionally, IAV infection increased serum concentrations of total protein, albumin and lipase, while decreasing the contents of calcium, triglyceride, total bilirubin, direct bilirubin, indirect bilirubin and gamma-glutamyltransferase. However, the interactions between the respiratory microbiome and metabolites and their impact on IAV in children remains unclear. Ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) and 16S rRNA gene sequencing were employed to analysis the respiratory microbiome and serum metabolic characteristics of 85 patients with IAV infection and age-matched 55 controls with respiratory disease who tested negative for 13 types of respiratory pathogens. The serum metabolic profile of IAV patients was significantly changed, and the purine metabolism was destroyed. Purine metabolism was also enriched in H3N2 patients compared to H1N1, with increased xanthine, deoxyguanosine, and inosine. The respiratory microbiome structure in children with IAV, including H1N1 and H3N2, was significantly different from that of the control, with significantly increased Chao index. The Mantel test revealed the correlation and consistency in the trends of Haemophilus, Ureaplasma and Inosine. This study revealed the characteristics of the respiratory microbiome and serum metabolites in pediatric patients with IAV, providing a new direction for exploring the pathogenesis of IAV in children.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Influenza, Human/blood
*Metabolome
*Microbiota
Female
Male
Child, Preschool
Child
RNA, Ribosomal, 16S/genetics
Influenza A virus
Infant
Influenza A Virus, H1N1 Subtype
Influenza A Virus, H3N2 Subtype
Serum/chemistry
Adolescent
Mass Spectrometry
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