binned metagenome: spire_mag_01843348
Phocaeicola vulgatus
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01843348
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2010-08-02
completeness score
91.58
completeness software
checkm2 0.1.3
contamination score
3.51
environmental medium
stool
geographic location (country and/or sea)
USA
geographic location (latitude)
missing: third party data
geographic location (longitude)
missing: third party data
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
Extreme dysbiosis in the gastrointestinal microbiota is frequent in intensive care unit (ICU) patients. This dysbiosis is associated with increased risk of pathobiont colonization and healthcare-associated infections. Researchers have been increasingly interested in developing predictive microbiota disruption indices (MDIs) that could be used to identify patients at risk of poor health outcomes such as gastrointestinal colonization by drug-resistant bacteria or hospital-acquired infections. We used 16S rRNA gene sequencing and shotgun metagenomic sequencing of DNA extracted stool samples. The stool samples were collected on consecutive days. These samples and clinical/epidemiologic data were used to examine temporal patterns in the microbiome. We learned that the microbiota of ICU patients can fluctuate on a daily basis. Gastrointestinal domination by specific bacteria, which is considered a risk factor for infection, was common, variable, and due to both pathogens (e.g., Enterococcus) and commensal bacteria species (e.g., Lactobacillus). Fluctuations in the microbiota were generally what one would predict based on the specific taxa and resistance genes present and antibiotic(s) administered. The rapid changes in the GI microbiota have implications for the design of MDIs for patient monitoring.
sample derived from
SAMN12617466
sample name
spire_mag_01843348
scientific_name
Phocaeicola vulgatus
sequencing method
Illumina NovaSeq 6000
taxonomic identity marker
multi-marker approach