2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21056204
SRA accession
spire_mag_00148593
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
2011-01-17
collection date
100
%
completeness score
checkm2 0.1.3
completeness software
0.05
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic runs SRR3131966,SRR3131965 of study SRP069019.
description
stool
environmental medium
USA
geographic location (country and/or sea)
38.6375
DD
geographic location (latitude)
-90.2651
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
Dysbiotic colonization of the preterm infant gut microbiota may have lifelong effects on host health. The normal progression of colonization of preterm infants is a patterned, yet chaotic, process, and thought to be chiefly driven by host factors. While preterm infants almost universally receive early and often repeated and/or prolonged intravenous antibiotic therapy, it remains unclear if and how specific antibiotics alter the developmental progression of the gut microbiota in this population. By analyzing 401 fecal samples from 84 longitudinally-sampled preterm infants, we demonstrate that meropenem, cefotaxime, and ticarcillin-clavulanate significantly reduce species richness during their administration, and significantly enrich or deplete specific bacterial species and antibiotic resistance (AR) genes. In contrast, vancomycin and gentamicin, the antibiotics most commonly administered to preterm infants, have non-uniform effects on species richness. We show this response is predictable with 85% accuracy based on the relative abundance of only two bacterial species and two AR genes before treatment. To more fully investigate the role of the gut-associated resistome in response to specific antibiotics, we performed functional metagenomic selections for resistance to 16 clinically relevant antibiotics from a set of 21 preterm infants’ gut microbiota. Of the 794 AR genes identified, 79% had not previously been classified as providing any resistance phenotype. Combined with deep shotgun sequencing of all 401 fecal samples, we find that multidrug resistant Escherichia, Klebsiella, and Enterobacter species, which are commonly associated with nosocomial infections, dominate the preterm infant gut microbiota. We show that AR genes that are enriched following specific antibiotic treatments are generally unique to the specific treatment and highly correlated (p<0.001) with the abundance of a single species. The most notable exception includes ticarcillin-clavulanate and ampicillin, both of which enrich a large number of overlapping AR genes, and are highly correlated with Klebsiella pneumoniae species in the preterm infant gut microbiota. In addition to AR genes relevant to specific antibiotics likely providing a protective function, we show that all antibiotic treatments also result in widespread collateral microbiome impact through enrichment of AR genes with no known direct activity against the specific antibiotic treatment.
project name
SAMN04436752
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00148593
title