2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21060539
SRA accession
spire_mag_01048809
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
61.38
%
completeness score
checkm2 0.1.3
completeness software
0.11
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic runs SRR726568,SRR651290,SRR649915,SRR648618,SRR649924,SRR606597,SRR649986,SRR651322,SRR649965 of study SRP001634.
description
not specified
environmental medium
not provided
geographic location (country and/or sea)
not provided
DD
geographic location (latitude)
not provided
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
The microbial composition of the gut likely contributes to a wide-range of health and disease states including intestinal inflammation, atopic disease, and possibly diseases of adulthood, such as heart disease and obesity. The early establishment of the gut microflora is suspected to have a particularly profound impact protecting the gut from infectious disease and on long-term subsequent health by predisposing individuals to atopic or autoimmune disease later in life. In contrast to the large-scale efforts of the Human Microbiome Project to characterize the microbial flora of healthy adults, relatively little has been accomplished to characterize the early establishment of the microbiota in infants. <p> The administration of antibiotics to infants has the capacity to profoundly affect the early acquisition, establishment, and natural maturation of commensal microflora. Prematurity is another major factor that is thought to influence 'normal' gut microbial composition in early life. A high number of pre-term infants receive antibiotic therapy prophylactically the immediate and long-term effects of antibiotic treatment on infant and later health outcomes are unknown. We hypothesize that gestational age influences the ability to support 'normal' gut microbiota, and that antibiotic administration in the first few weeks of life can alter or delay the development of a 'normal' microbiota and may lead to adverse health outcomes. If we hope to promote the healthy establishment of early gut colonization and thereby improve health outcomes, we need to establish what 'normal' colonization looks like across gestational ages and apply this knowledge as a benchmark to understand the impact of antibiotic treatment in early postnatal life. <p> In this project, we propose to examine the microbiome in four cohorts ranging from extremely preterm to term, with birth weights appropriate for gestational age: Group 1) 23 to 27 weeks and extremely low birth weight [ELBW, <1000 grams] Group 2) 28 to 32 weeks and very low birth weight [VLBW, >1000 to <1500 grams] Group 3) 33 to 36 weeks and low birth weight [LBW, >1500 to <2500 grams] and Group 4) term (37 to 42 weeks) and normal [>2500 to <4000 gram] birth weight. The infant gut microbiome will be assessed longitudinally in study infants from the first postnatal week to 18 months of age, and will include untreated and antibiotic-treated infants.
project name
SAMN01780043
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2000,Illumina HiSeq 2000,Illumina HiSeq 2000,Illumina MiSeq,Illumina HiSeq 2000,Illumina MiSeq,Illumina HiSeq 2000,Illumina HiSeq 2000,Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01048809
title