2024-09-19
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21061671
SRA accession
spire_mag_01405565
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
2017-10-18T00:00:00Z
collection date
90.89
%
completeness score
checkm2 0.1.3
completeness software
7.1
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR9199500 of study SRP200375.
description
stool
environmental medium
USA
geographic location (country and/or sea)
39.57000000
DD
geographic location (latitude)
-75.11000000
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
We applied metagenomic sequencing to respiratory and gastrointestinal tract specimens, collected from a cohort of long-term acute care hospital (LTACH) residents, in order to define microbiome and resistome change under antibiotic pressure, generate microbiome disruption indices (MDIs) to predict risk for multidrug-resistant infection, and contribute to a deeper understanding of how antibiotics and other medications increase risk of specific AMR gene selection and persistence.
project name
SAMN11954378
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01405565
title