2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21058192
SRA accession
spire_mag_00810691
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
70.98
%
completeness score
checkm2 0.1.3
completeness software
0.34
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR9865588 of study SRP216871.
description
stool
environmental medium
USA
geographic location (country and/or sea)
38.63750000
DD
geographic location (latitude)
-90.26530000
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
Because hospitalized preterm infants are vulnerable to infection, they receive frequent and often prolonged exposures to antibiotic therapy. It is not known if the demonstrated short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic and culture based techniques to interrogate the gut microbiota and resistome of antibiotic-exposed preterm infants both during, and after, hospitalization, and compare these readouts to antibiotic-naïve healthy infants sampled synchronously. We find an enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug resistant Enterobacteriaceae, and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants who received early life antibiotics. Our results demonstrate persistent collateral damage of early life antibiotic treatment and hospitalization in preterm infants and highlight the need for alternative strategies for infection management in highly vulnerable neonatal populations.
project name
SAMN09980867
sample derived from
Phocaeicola vulgatus
scientific_name
NextSeq 500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_00810691
title