U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Metagenome-assembled genome: SRR492196_bin.19_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14085768; SRA: ERS11688899
Organism
Enterococcus faecalis
cellular organisms; Bacteria; Bacillati; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus
Attributes
collection datenot provided
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationnot provided
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameStool sample from a premature human infant (UC1). <p> This study used metagenomic methods (community genomic analysis and sequencing of amplified 16S rRNA genes) to document microbial colonization of the gut of a premature infant born at 28 weeks gestation. Analysis of 16S rRNA gene sequences collected approximately daily revealed three compositional phases during colonization. We reconstructed genomes of the dominant organisms and intensively curated population genomic datasets from the third phase. In the third phase, the communities were dominated by a nearly clonal Serratia population, two Citrobacter strains sharing >99% nucleotide identity, and contained a lower abundance Enterococcus population, multiple plasmids and bacteriophage. The relative abundance of the Citrobacter strains changed significantly over time. Modeling of Citrobacter strain abundances suggests differences in growth rates and/or host colonization patterns. We identified genotypic variation potentially responsible for divergent strain ecologies, including hotspots of sequence variation in regulatory genes and intergenic regions, and in genes involved in transport, flagellar biosynthesis, substrate metabolism, and host colonization, as well as differences in the complements of these genes. Our results demonstrate that a community genomic approach can elucidate gut microbial colonization at the resolution required to discern medically relevant strain and species population dynamics, and hence improve our ability to diagnose and treat microbial community-mediated disorders.
sample nameSRR492196_bin.19_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14085768
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:32Z
INSDC last update2023-01-03T00:33:32Z
INSDC statuspublic
Submitter IdSRR492196_bin.19_CONCOCT_v1.1_MAG
assembly qualityMultiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly softwaremetaSPAdes version 3.10.139
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score99.63
completeness softwareCheckM
contamination score0.0
geographic location (latitude)not provided
geographic location (longitude)not provided
metagenomic sourcehuman gut metagenome
sample derived fromSAMN00990124
scientific_nameEnterococcus faecalis
sequencing methodIllumina HiSeq 2000
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR492196 of study SRP012558.

BioProject
PRJEB51075 Large-scale analysis of novel cellular microbes from the human gut biome
Retrieve all samples from this project

Submission
EBI; 2023-01-04
Accession:
SAMEA14085768
ID:
32562394

BioProject Nucleotide

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center