2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21058252
SRA accession
spire_mag_00832279
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
missing: third party data
collection date
94.09
%
completeness score
checkm2 0.1.3
completeness software
1.79
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR769414 of study SRP019038.
description
stool
environmental medium
USA
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
Associating the biomolecular and metabolic activities of human-associated microbial communities with environment, diet, and conditions such as inflammatory bowel disease remains a significant challenge despite an ever-improving understanding of the human microbiome. This project aims to pilot detection of taxonomic and functional shifts with respect to diet and gastrointestinal disease status in a large prospective cohort: 1. We will establish a reliable and scalable collection method for the oral and gut microbiota. This will determine whether shippable collection kits are comparable to fresh frozen stool and/or saliva samples. 2. We will test the hypothesis that a Western dietary pattern correlates with microbiome community structures or functions enriched in inflammatory bowel disease in either the oral (saliva) or gut (stool) microbiota. By providing methodology to understand the human microbiome from the molecular to the population level, we hope to enable its future use as a diagnostic indicator and as a point of intervention to improve outcomes in IBD and other chronic diseases.
project name
SAMN01915211
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00832279
title