Bacteroides uniformis
ENA first public
2024-09-21
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01841272
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
2013
completeness score
81.73
completeness software
checkm2 0.1.3
contamination score
0.23
environmental medium
stool
geographic location (country and/or sea)
USA
geographic location (latitude)
29.77152983
geographic location (longitude)
-95.22124444
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
Human microbial communities are characterized by their metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, it is not yet known when in early development our microbiota community structure and function is initially established and diversifies. We thus sought to assess the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota, and assess the impact of mode of delivery and its potential confounders or modifiers. A cohort of pregnant women (n=81) were prospectively enrolled for longitudinal sampling through 6 weeks post-delivery, and a second matched cross-sectional cohort (n=81) was additionally recruited for sampling once at delivery. Samples were collected for each maternal-infant dyad across multiple body sites, including stool, oral gingiva, nares, skin and vagina. 16S rRNA gene sequencing analysis and whole genome shotgun sequencing was performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogenous across all body sites at delivery, with the notable exception of neonatal meconium. However, by 6 weeks, the infant microbiota structure and function had significantly expanded and diversified, with body site serving as the primary determinant of the bacterial community composition and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with Cesarean delivery in some body sites (oral, nares, and skin p<0.001, R2 = 0.038), this was not true in neonatal stool (meconium) and there was no observable difference in community function regardless of delivery mode. By 6 weeks of age, the infant microbiota structure and function had expanded and diversified with demonstrable body site specificity (p<0.001, R2 = 0.189), and no discernable differences in neither community structure nor function by Cesarean delivery were identifiable (p=0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes significant reorganization that is primarily driven by body site and not by mode of delivery.
sample derived from
SAMN05525394
sample name
spire_mag_01841272
scientific_name
Bacteroides uniformis
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach