2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21061357
SRA accession
spire_mag_01270940
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
2012
collection date
90.43
%
completeness score
checkm2 0.1.3
completeness software
0.3
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR589756 of study ERP006678.
description
stool
environmental medium
China
geographic location (country and/or sea)
55.67609700
DD
geographic location (latitude)
12.56833700
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
Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier.
project name
SAMEA2737761
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01270940
title