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Metagenome-assembled genome: SRR3546782_bin.2_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14036179; SRA: ERS11639461
Organism
Candida albicans
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Pichiomycetes; Serinales; Debaryomycetaceae; Candida/Lodderomyces clade; Candida
Attributes
collection date2012-04-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationUSA
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameBacteria that persist in hospitals can contribute to the establishment of the microbiome in newborns and the spread of hospital-acquired diseases. Yet we know little about microbial communities in hospitals, or about the extent to which persistent vs. recently immigrated bacterial strains establish in the gastrointestinal tracts of hospitalized individuals.</p><p>In combination with BioProject PRJNA273761 (10 infants / 55 samples) we analyzed strain-resolved genomes obtained from a total of 202 samples collected over a three-year period from 21 infants hospitalized in the same intensive care unit.</p><p>Strains were rarely shared, consistent with prior analysis of a subset of these data. Enterococcus faecalis and Staphylococcus epidermidis, common gut colonists, exhibit diversity comparable to that of NCBI reference strains, suggesting no recent common ancestor for all populations in this hospital setting. Thus, we infer multiple introduction events for these species. Despite the rarity of shared strains, strains of five species exhibiting a degree of sequence variation consistent with in situ diversification were identified in different infants hospitalized three years apart. Three were also detected in multiple infants in the same year, suggesting that these strains are unusually widely dispersed and persistent in the hospital environment. Persistent strains were not significantly different from non-persistent strains with regards to pathogenicity potential including antibiotic resistance. Notably, non-identical siblings had multiple abundant strains in common, even 30 days after birth and antibiotic administration, suggesting overlapping strain sources and/or genetic selection. Our approach can be used in order to study microbial dynamics in hospitals and provides an important step towards directing health-promoting colonization in hospitalized individuals.
sample nameSRR3546782_bin.2_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14036179
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 IdSRR3546782_bin.2_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspadesv3.11.1
binning parametersDefault
binning softwareCONCOCT v1.1, EukCC2
broker nameEMG broker account, EMBL-EBI
completeness score98.76
completeness softwareCheckM
contamination score0.21
geographic location (latitude)40.4308
geographic location (longitude)-79.9598
metagenomic sourcehuman gut metagenome
sample derived fromSAMN04161035
scientific_nameCandida albicans
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 SRR3546782 of study SRP074153.

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:
SAMEA14036179
ID:
32555587

BioProject Nucleotide

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