Metagenome-assembled genome: SRR492196_bin.19_CONCOCT_v1.1_MAG
Enterococcus faecalis
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR492196 of study SRP012558.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14085768
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:32Z
INSDC last update
2023-01-03T00:33:32Z
INSDC status
public
Submitter Id
SRR492196_bin.19_CONCOCT_v1.1_MAG
assembly quality
Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly software
metaSPAdes version 3.10.139
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
not provided
completeness score
99.63
completeness software
CheckM
contamination score
0.0
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
not provided
geographic location (latitude)
not provided
geographic location (longitude)
not provided
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
Stool sample from a premature human infant (UC1). &lt;p&gt; 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 &gt;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 derived from
SAMN00990124
sample name
SRR492196_bin.19_CONCOCT_v1.1_MAG
scientific_name
Enterococcus faecalis
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach