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Metagenome-assembled genome: SRR1779153_bin.70_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14036178; SRA: ERS11639460
Organism
Candida parapsilosis
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; CUG-Ser1 clade; Debaryomycetaceae; Candida/Lodderomyces clade; Candida
Attributes
collection date2014-07-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationUSA
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project namePremature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. This study compares microbial communities of 10 co-hospitalized infants, five of which had a diagnosis of necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, a genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants that developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically-relevant time scales.
sample nameSRR1779153_bin.70_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14036178
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:32:14Z
INSDC last update2023-01-03T00:32:14Z
INSDC statuspublic
Submitter IdSRR1779153_bin.70_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspadesv3.10.0
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score99.79
completeness softwareCheckM
contamination score0.0
geographic location (latitude)40.4308
geographic location (longitude)-79.9598
metagenomic sourcehuman gut metagenome
sample derived fromSAMN03295858
scientific_nameCandida parapsilosis
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 SRR1779153 of study SRP052967.

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:
SAMEA14036178
ID:
32555586

BioProject Nucleotide

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