2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21057914
SRA accession
spire_mag_00737845
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
2016-05-20
collection date
84.65
%
completeness score
checkm2 0.1.3
completeness software
4.67
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR2262426 of study ERP106388.
description
stool
environmental medium
Switzerland
geographic location (country and/or sea)
46.91670000
DD
geographic location (latitude)
7.46670000
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
Purpose: Retinal artery occlusion usually occurs on a background of atherosclerotic disease and patients are at risk for cerebral stroke and ischemic heart disease. Atherosclerosis has been associated with alterations in the intestinal microbiome. Methods: Twenty nine patients with clinically confirmed non-arteritic retinal artery occlusion and 30 age- and sex-matched controls were included. The gut metagenome was sequenced using metagenomic shotgun sequencing following standard pipelines of the Illumina HiSeq 3000 platform. The taxonomic composition of the gut microbiomes was described and the functional profiles of the identified microbes were identified. Results: On the phylum level, the relative abundance of Bacteriodetes was decreased in patients with retinal artery occlusion (39.2 ± 16.7%) compared to controls (46.7 ± 17.6%) whereas the opposite applied for the phylum of Firmicutes (39.6 ± 20.0% in RAO and 40.8 ± 16.0% (s.d.) in controls). Several genera and species such as Actinobacter, Bacteroides stercoris, Faecalibacterium prausnitzii were relatively enriched in patients with retinal artery occlusion, whereas others such as Odoribacter or Lachnospiraceae were significantly lower. Patient’s gut microbiomes were enriched in genes of the cholesterol metabolism pathway. Conclusions: Alterations in the gut microbiome are associated with retinal artery occlusion, suggesting that retinal artery occlusion could be targeted by microbiome-altering interventions.
project name
SAMEA104500083
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 3000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00737845
title