2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21062517
SRA accession
spire_mag_01628726
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
85.66
%
completeness score
checkm2 0.1.3
completeness software
1.76
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR9879814 of study SRP217052.
description
stool
environmental medium
not provided
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
Microbial colonization and succession in the gut of human infants are linked to health and disease later in life. Although the taxonomic and functional characteristics of the infant microbiome just after birth have been extensively investigated, we are just beginning to decipher its impact on the biochemical environment. To examine this, we characterized the microbiome, proteome, and metabolome of meconium samples from 88 newborn infants. Using shotgun metagenomic DNA sequencing, we found that human DNA accounted for >75% of sequence reads in 52 samples. High levels of human DNA were found preferentially in samples collected within 16 hours of birth. Quantification by 16S qPCR confirmed that absolute bacterial abundance was low in samples with high human DNA. Escherichia coli, Enterococcus faecalis, and Bacteroides vulgatus were the most commonly detected species, and they did not exhibit a strong phylogenetic or pan-genome signature unique to meconium. The number of strains increased with time after birth at a rate of 1.2 strains per day
project name
SAMN12418483
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01628726
title