Bacteroides uniformis
ENA first public
2024-09-21
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01628357
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
missing: third party data
completeness score
54.52
completeness software
checkm2 0.1.3
contamination score
0.4
environmental medium
stool
geographic location (country and/or sea)
not provided
geographic location (latitude)
missing: third party data
geographic location (longitude)
missing: third party data
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
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
sample derived from
SAMN12418424
sample name
spire_mag_01628357
scientific_name
Bacteroides uniformis
sequencing method
Illumina HiSeq 2500
taxonomic identity marker
multi-marker approach