Mouse microbiomes and viromes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA970614 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24860700_1.fastq.gz | Fastqsanger.gz | |||
| SRR24860700_2.fastq.gz | Fastqsanger.gz | |||
| SRR24860701_1.fastq.gz | Fastqsanger.gz | |||
| SRR24860701_2.fastq.gz | Fastqsanger.gz | |||
| SRR24860702_1.fastq.gz | Fastqsanger.gz |
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Project description:Ulcerative colitis is a chronic inflammatory disorder for which a definitive cure is still missing. This is characterized by an overwhelming inflammatory milieu in the colonic tract where a composite set of immune and non-immune cells orchestrate its pathogenesis. Over the last years, a growing body of evidence has been pinpointing gut virome dysbiosis as underlying its progression. Nonetheless, its role during the early phases of chronic inflammation is far from being fully defined. Here we show the gut virome-associated Hepatitis B virus protein X, most likely acquired after an event of zoonotic spillover, to be associated with the early stages of ulcerative colitis and to induce colonic inflammation in mice. It acts as a transcriptional regulator in epithelial cells, provoking barrier leakage and altering mucosal immunity at the level of both innate and adaptive immunity. This study paves the way to the comprehension of the aetiopathogenesis of intestinal inflammation and encourages further investigations of the virome as a trigger also in other scenarios. Moreover, it provides a brand-new standpoint that looks at the virome as a target for tailored treatments, blocking the early phases of chronic inflammation and possibly leading to better disease management.
2023-02-20 | GSE204665 | GEO
Project description:Virome biogeography in the primate lower gastrointestinal tract
| PRJNA491509 | ENA
Project description:We have previously demonstrated that the gut microbiota can play a role in the pathogenesis of conditions associated with exposure to environmental pollutants. It is well accepted that diets high in fermentable fibers such as inulin can beneficially modulate the gut microbiota and lessen the severity of pro-inflammatory diseases. Therefore, we aimed to test the hypothesis that hyperlipidemic mice fed a diet enriched with inulin would be protected from the pro-inflammatory toxic effects of PCB 126.
2020-02-27 | E-MTAB-8798 | biostudies-arrayexpress
Project description:Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.
| S-EPMC9397868 | biostudies-literature
Project description:Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.
| S-EPMC11786891 | biostudies-literature
Project description:Acute stress provides many beneficial effects whereas chronic stress contributes to a variety of human health problems. The objective of this study was to use a rodent model to uncover hippocampal gene signatures associated with prolonged chronic stress which could potentially serve as biomarkers and therapeutic targets for early diagnosis and pharmacological intervention for stress induced disease. Mice were subjected to restraint stress over 7 consecutive days and gene expression changes in the hippocampus were analyzed at 3, 12 and 24 hours following the final restraint treatment. Data indicated that mice exposed to chronic restraint stress exhibit a differential gene expression profile compared to non-stressed controls. The greatest differences were observed 12 and 24 hrs following the final stress test.
2016-11-02 | E-MTAB-2402 | biostudies-arrayexpress
Project description:Understanding the transmission of antibiotic resistance genes (ARGs) is critical for human health. For this, it is necessary to identify which type of mobile genetic elements is able to spread them from animal reservoirs into human pathogens. Previous research suggests that in pig feces, ARGs may be encoded by bacteriophages. However, convincing proof for phage-encoded ARGs in pig viromes is still lacking, because of bacterial DNA contaminating issues. We collected 14 pig fecal samples and performed deep sequencing on both highly purified viral fractions and total microbiota, in order to investigate phage and prophage-encoded ARGs. We show that ARGs are absent from the genomes of active, virion-forming phages (below 0.02% of viral contigs from viromes), but present in three prophages, representing 0.02% of the viral contigs identified in the microbial dataset. However, the corresponding phages were not detected in the viromes, and their genetic maps suggest they might be defective. We conclude that among pig fecal samples, phages and prophages rarely carry ARG. Furthermore, our dataset allows for the first time a comprehensive view of the interplay between prophages and viral particles, and uncovers two large clades, inoviruses and Oengus-like phages.
| S-EPMC9723715 | biostudies-literature
Project description:An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.
| S-EPMC5492393 | biostudies-literature
Project description:Recent studies have demonstrated that chronic stress can enhance the development of multiple human diseases, including cancer. However, the role of chronic stress in esophageal carcinogenesis and its underlying molecular mechanisms remain unclear. This study uncovered that dysregulated cholesterol metabolism significantly promotes esophageal carcinogenesis under chronic stress conditions. Our findings indicate that the persistent elevation of glucocorticoids induced by chronic stress stimulates cho-lesterol uptake, contributing to esophageal carcinogenesis. The activated glucocor-ticoid receptor (GCR) enrichment at the promoter region of High Mobility Group Box Protein 2 (HMGB2) facilitates its transcription. As a transcription co-activator, HMGB2 enhances Sterol Regulatory Element-Binding Transcription Factor 1 (SREBF1) transcription and regulates cholesterol metabolism through LDL particle uptake into cells via Low-Density Lipoprotein Receptor (LDLR). These results em-phasize the significant impact of chronic stress on esophageal carcinogenesis and establish cholesterol metabolism disorder as a crucial link between chronic stress and the development of ESCC. The implications suggest that effectively managing chronic stress may serve as a viable strategy for preventing and treating ESCC.
2025-01-13 | GSE286200 | GEO
Project description:Aims: The sympathetic nervous system regulates numerous critical aspects of mitochondrial function in the heart through activation of adrenergic receptors (ARs) on cardiomyocytes. Chronic β-AR activation causes maladaptive alterations in cardiomyocyte metabolism that contribute to the pathobiology of heart failure. In contrast, mounting evidence suggests that a1-ARs, particularly the a1A subtype, are cardioprotective and may mitigate the deleterious effects of chronic β-AR activation by shared endogenous catecholamine ligands. The mechanisms through which a1A-ARs exert their cardioprotective effects remain unclear. Here we tested the hypothesis that a1A-ARs adaptively regulate cardiomyocyte oxidative metabolism in both the uninjured and failing heart.
Methods: We characterized the effects of global α1A-AR genetic deletion on mitochondrial function and metabolism in the uninjured mouse heart using high resolution respirometry, substrate-specific electron transport chain (ETC) enzyme assays, transmission electron microscopy (TEM), proteomics, and lipidomics. We then compared the effects of α1A- and β-AR agonist treatment on ETC enzyme activity and oxidative stress in vivo and in vitro. We subjected wild type and cardiomyocyte-specific α1A-KO mice to permanent left coronary artery (LCA) ligation and used RNAseq to compare the transcriptomic response. Results: We found that isolated cardiac mitochondria from mice with global α1A-AR genetic deletion (α1A-KO) had deficits in fatty acid-dependent respiration and ETC enzyme activity. TEM revealed abnormalities of mitochondrial morphology characteristic of these functional deficits. The selective α1A-AR agonist A61603 (100 ng/kg/d, 3d) enhanced fatty acid oxidation (FAO) in isolated cardiac mitochondria while increasing expression and activity of the mitochondrial trifunctional protein, a critical FAO mediator. The β-AR agonist isoproterenol enhanced oxidative stress in vitro and this adverse effect was mitigated by A61603. RNAseq revealed broad basal deficits in pathways related to mitochondria and OXPHOS in cardiomyocyte-specific α1A-KO mice; these differences were exaggerated by LCA ligation. A61603 enhanced ETC Complex I activity and protected contractile function following myocardial infarction.
Conclusions: Collectively, these novel findings position α1A-ARs as critical regulators of cardiomyocyte metabolism in the basal state and suggest that metabolic mechanisms may underlie the protective effects of α1A-AR activation in the failing heart.
2024-08-15 | PXD044591 | JPOST Repository