Metagenome-assembled genome: SRR3546782_bin.35_CONCOCT_v1.1_MAG
uncultured Actinomyces sp.
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR3546782 of study SRP074153.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14085705
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:40Z
INSDC last update
2023-01-03T00:33:40Z
INSDC status
public
Submitter Id
SRR3546782_bin.35_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspadesv3.11.1
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
2012-04-01
completeness score
99.29
completeness software
CheckM
contamination score
0.95
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
USA
geographic location (latitude)
40.4308
geographic location (longitude)
-79.9598
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
Bacteria 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.&lt;/p&gt;&lt;p&gt;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.&lt;/p&gt;&lt;p&gt;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 derived from
SAMN04161035
sample name
SRR3546782_bin.35_CONCOCT_v1.1_MAG
scientific_name
uncultured Actinomyces sp.
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach