2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21062928
SRA accession
spire_mag_01778139
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
93.25
%
completeness score
checkm2 0.1.3
completeness software
1.1
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR2505999 of study ERP105801.
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
Neonates at heightened risk of childhood atopy and asthma are characterized by inter-kingdom perturbation of their gut microbiota and metabolic dysfunction that includes fecal enrichment of the linoleic acid metabolite, 12,13 DiHOME1. Treatment of human dendritic cells (DCs) with this oxylipin decreased IL-10, altered expression of peroxisome-proliferator-activated-receptor-γ (PPARγ)-regulated genes, and decreased regulatory T cell (Tregs) frequency ex vivo. Mice treated with 12,13 DiHOME and subjected to a model of airway allergic sensitization had exacerbated pulmonary inflammation and decreased lung Tregs. Fecal metagenomic sequencing from neonates who developed atopy and/or asthma revealed a significant increase in bacterial epoxide hydrolase (EH) genes. Three of these bacterial EHs can produce 12,13 DiHOME in vitro. The abundance of fecal oxylipins and bacterial EH genes in neonatal stool can be combined with known early-life risk factors to predict neonatal risk of atopy at age two and asthma at age four.
project name
SAMEA1069181
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 4000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01778139
title