Shotgun metagenomic sequencing of infant gut microbiota - SRA

SRX6619358: Shotgun metagenomic sequencing of infant gut microbiota
1 ILLUMINA (NextSeq 500) run: 5M spots, 1.1G bases, 524.1Mb downloads

Design: Metagenomic DNA was extracted from approximately 100 mg of stool samples using the PowerSoil DNA Isolation Kit (MoBio Laboratories) following the manufacturers protocol with the following modification: samples were lysed by two rounds of two minutes of bead beating at 2.5k oscillations per minute for 2 minutes followed by 1 minute on ice and 2 additional minutes of beadbeating using a Mini-Beadbeater-24 (Biospec Products). DNA was quantified using a Qubit fluorometer dsDNA BR Assay (Invitrogen) and stored at -20?C. Metagenomic DNA was diluted to a concentration of 0.5 ng/L prior to sequencing library preparation. Libraries were prepared using a Nextera DNA Library Prep Kit (Illumina) following the modifications described in Baym et al, 20153. Libraries were purified using the Agencourt AMPure XP system (Beckman Coulter) and quantified using the Quant-iT PicoGreen dsDNA assay (Invitrogen). For each sequencing lane, 10 nM of approximately 96 samples were pooled three independent times. These pools were quantified using the Qubit dsDNA BR Assay and combined in an equimolar fashion. Samples were submitted for 2150 bp paired-end sequencing on an Illumina NextSeq High-Output platform at the Center for Genome Sciences and Systems Biology at Washington University in St. Louis with a target sequencing depth of 2.5 million reads per sample.

Submitted by: Washington University in St. Louis

Study: Human infant gut metagenome, infant shotgun sequencing

PRJNA489090 • SRP216871 • All experiments • All runs

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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.

Sample:

SAMN09980693 • SRS5179632 • All experiments • All runs

Organism: human gut metagenome

Library:

Name: N037.A

Instrument: NextSeq 500

Strategy: WGS

Source: METAGENOMIC

Selection: RANDOM

Layout: PAIRED

Runs: 1 run, 5M spots, 1.1G bases, 524.1Mb

Run	# of Spots	# of Bases	Size	Published
SRR9865766	4,997,566	1.1G	524.1Mb	2019-10-05

ID:: 8729956

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