Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human gut metagenome

ABSTRACT: Genome reconstructions from human gut metagenomes

PROVIDER: PRJNA312222 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	LWLH01.dat.gz	Other
	LWLH01.fasta.gz	Fasta.gz
	LWLH01.master.dat	Other
	LWLI01.dat.gz	Other
	LWLI01.fasta.gz	Fasta.gz

Items per page:

1 - 5 of 44

Similar Datasets

Relating human gut metagenome and metaproteome

Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.

2017-07-19 | PXD005780 | Pride

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Project description:Human DNA present in fecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is currently unclear how much personal information can be reconstructed from such reads and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable the efficient use of human genetic information in stool samples, such as for research and forensics. Here, we used genomic approaches to reconstruct personal information from fecal metagenomes of 343 Japanese individuals with associated human genotype data. Our approach can be used to quantify the personal information contained within gut metagenome data.

| EGAS00001007027 | EGA

gut metagenome

Project description:Metagenomic Reconstructions of Gut Microbiome in Weanling Pigs

| PRJNA494875 | ENA

Reanalysis of dataset PXD005780: “Relating human gut metagenome and metaproteome”

Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD005780. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 15,417 unique proteins from 15 samples.

2022-05-04 | PXD032303 | Pride

human gut metagenome

Project description:Gut metagenomes of patients with COVID-19

| PRJNA650244 | ENA

human gut metagenome

Project description:preterm infant gut metagenomes (NIH Y4 Cohort)

| PRJNA396794 | ENA

human gut metagenome

Project description:Gut metagenomes of patients with colorectal cancer

| PRJNA397219 | ENA

human gut metagenome

Project description:preterm infant gut metagenomes (S2_2013 and NIHY2_2012 cohorts)