binned metagenome: spire_mag_02695499
Phocaeicola vulgatus
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_02695499
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
2016-07-02
completeness score
52.78
completeness software
checkm2 0.1.3
contamination score
0.15
environmental medium
stool
geographic location (country and/or sea)
USA
geographic location (latitude)
33.45480560
geographic location (longitude)
-112.36427778
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
Microbial ecology has witnessed tremendous progress over the last decade empowered by new sequencing technologies. These innovations in DNA sequencing resulted in a paradigm shift concerning our understanding of pathogenic processes and gave birth to a new scientific concept, namely the “pathobiome”. In the pathobiome concept, the microbial community containing a pathogenic agent exerts a major influence on the persistence, transmission and evolution of the pathogen. It is therefore mandatory to identify those species that contribute, either as partners or antagonists, to pathogen's survival, extinction or dispersal by applying concepts and approaches of systems biology. Developing multi-meta-omic systems biology frameworks would allow us to go beyond the identification of mere statistical co-occurrence patterns and instead develop computational models that describe the spatio-temporal dynamics of the pathogen and the functional interactions with its biotic environment. To demonstrate the power of our approach, we will use systems level analysis and modelling to investigate the contribution of the biotic environment to the colonization and dissemination of Candida albicans.
sample derived from
SAMEA5818160
sample name
spire_mag_02695499
scientific_name
Phocaeicola vulgatus
sequencing method
unspecified
taxonomic identity marker
multi-marker approach