Nitrofurantoin Metagenomics study
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR753686.fastq.gz | Fastqsanger.gz | |||
| ERR753687.fastq.gz | Fastqsanger.gz | |||
| ERR753688.fastq.gz | Fastqsanger.gz | |||
| ERR753689.fastq.gz | Fastqsanger.gz | |||
| ERR753690.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 37 |
Similar Datasets
Project description:We recruited 24 Mongolian volunteers,6 of which were T2D cases(sample T1-T6), 6 were prediabetes cases(sample P1-P6), and 12 were health cases(sample C1-C12). The metagenomic analysis of gut microbiota from the volunteers’ fecal samples was performed. We compared the microbial differences in the three groups, and analyzed the differences of the stool microbial function.
2022-07-30 | E-MTAB-11957 | biostudies-arrayexpress
Project description:Nitrofurantoin heteroresistance in Escherichia coli
| PRJEB58678 | ENA
Project description:This study explores the role of the gut microbiome in modulating host metabolism among Colombian athletes, comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis using bioBakery tools identified significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation (Figure 1). Key metabolic pathways were enriched in both athlete groups, such as phenylalanine, tyrosine, and tryptophan biosynthesis, arginine biosynthesis, and folate biosynthesis. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between gut microbiota composition and metabolic responses tailored to athletic demands, laying groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.
2024-11-20 | MSV000096474 | MassIVE
Project description:To unravel distinct pattern of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and explore the impact of COVID-19 pandemic on epidemiological features
2024-08-07 | GSE274269 | GEO
Project description:The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients. In our study, we compared fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively by using next-generation sequencing targeting 16S ribosomal RNA. Then, shotgun metagenomic sequencing was firstly used to characterize bacterial gut microbial communities and related functional change in AT group. We found that the diversity and structure of the microbial community in AT group were significantly changed compared to that of BT group and H group. AT group showed a microbiota profile characterized by increased proportions of the phylum Firmicute, families Ruminococcaceae, and a reduction in the phylum Bacteroidota (elevated F/B ratio). To detect functional alteration, we discovered that secukinumab treatment may construct a more stable homeostasis of gut microbiome with functional alteration. There were different KEGG pathways such as downregulated cardiovascular diseases pathway and upregulated infectious diseases in AT group. By metagenomic analysis, metabolic functional pathway was changed after secukinumab therapy. It seems that gut microbiota investigation during biologic drug treatment is useful for predicting the efficacy and risks of drug treatment in disease.
2023-08-07 | GSE239719 | GEO
Project description:The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients. In our study, we compared fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively by using next-generation sequencing targeting 16S ribosomal RNA. Then, shotgun metagenomic sequencing was firstly used to characterize bacterial gut microbial communities and related functional change in AT group. We found that the diversity and structure of the microbial community in AT group were significantly changed compared to that of BT group and H group. AT group showed a microbiota profile characterized by increased proportions of the phylum Firmicute, families Ruminococcaceae, and a reduction in the phylum Bacteroidota (elevated F/B ratio). To detect functional alteration, we discovered that secukinumab treatment may construct a more stable homeostasis of gut microbiome with functional alteration. There were different KEGG pathways such as downregulated cardiovascular diseases pathway and upregulated infectious diseases in AT group. By metagenomic analysis, metabolic functional pathway was changed after secukinumab therapy. It seems that gut microbiota investigation during biologic drug treatment is useful for predicting the efficacy and risks of drug treatment in disease.
2023-08-07 | GSE239720 | GEO
Project description:Background: As a worldwide threat to mental health, depression affects about 322 million people globally. Recently, the role of gut microbiota dysbiosis on the pathogenesis of depression has received widespread attention, but the underlying mechanism remains elusive.Results: Corticosterone (CORT)-treated mice showed depressive-like behaviors, a reduction in hippocampal neurogenesis, and an altered composition of gut microbiota (GM). Fecal microbial transplantation (FMT) from CORT-treated mice transferred depressive-like phenotypes and their dominant GM, especially bifidobacterium and lactobacillus, to the recipients. Fecal metabolic profiling showed that the relative abundances of fecal ceramides were significantly increased in CORT-treated and the recipient mice. Metagenomic sequencing exposed that bifidobacterium and lactobacillus might be responsible for gut ceramides production in CORT-treated mice. We then found that treatment with ceramides via oral gavage was sufficient to recapitulate the depressive-like phenotypes in wild -type mice. Finally, RNA-sequencing data exposed that most of the differentially expressed genes (DEGs) between ceramides-treated mice and the control group were enriched in oxidative phosphorylation (OXPHOS) pathway. Conclusion: We conclude that chronic exposure to CORT leads to an altered GM composition and consequent ceramides production, thus leading to subtle mitochondrial OXPHOS dysfunction in hippocampus, which may contribute to the development of depressive disorders.
2024-04-01 | GSE229237 | GEO
Project description:We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humansM-bM-^@M-^Y age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. Further analysis indicated that antibiotic resistance genes in groups of CH, SC and AD can be independently clustered, and those ones in group HSS are more divergent. The detailed analysis of antibiotic resistance genes in human gut is further described in the paper DNA microarray analysis reveals the antibiotic resistance gene diversity in human gut microbiota is age-related submitted to Sentific Reports The antibiotic resistance gene microarray is custom-designed (Roche NimbleGen), based on a single chip containing 3 internal replicated probe sets of 12 probes per resistance gene, covering the whole 315K 12-plex platform spots.
2014-01-16 | E-GEOD-54070 | biostudies-arrayexpress
Project description:Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a high density custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals. Fecal samples were collected from eight female subjects. Three were obese subjects of BMI kg m-2: 35, 46.8 and 51.3, respectively; age: 42, 21 and 65 years old, respectively. Three were anorexic women of BMI kg m-2: 9.8, 10 and 13.7, respectively; age: 19, 23 and 49 years old, respectively. Finally, two fecal samples from lean women of BMI kg m-2: 18.6 and 23.42 were analyzed.
2013-10-28 | E-GEOD-51760 | biostudies-arrayexpress