Metagenome-assembled genome: ERR1543996_bin.47_CONCOCT_v1.1_MAG
uncultured Bacillota bacterium
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1543996 of study ERP015638.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14083611
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:32Z
INSDC last update
2023-01-03T00:33:32Z
INSDC status
public
Submitter Id
ERR1543996_bin.47_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
2013-09-01
completeness score
97.75
completeness software
CheckM
contamination score
0.0
environment (biome)
Host-associated
environment (feature)
Human
environment (material)
Digestive system
geographic location (country and/or sea)
Denmark
geographic location (latitude)
56.2639
geographic location (longitude)
9.5018
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
metagenomic source
human gut metagenome
project name
Diarrhoea is a major global disease burden and rapid, precise identification of the causative pathogens is important to initiate patient treatment and to discover and handle potential outbreaks. The current diagnostics involve numerous procedures and often the pathogen is not identified in time to guide clinical management. Furthermore, in many clinical cases pathogens are never identified. With next-generation sequencing (NGS) becoming cheaper it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included. DNA was extracted from faecal samples and sequenced on the Illumina MiSeq. Species distribution was determined with MGmapper (http://cge.cbs.dtu.dk/services/MGmapper/) and NGS-based diagnostic prediction was performed based on relative abundance of pathogenic bacteria and Giardia and detection of pathogen-specific virulence genes. NGS-based diagnostic results were compared to conventional findings for 55 of the diarrhoeal samples; 38 conventionally positive for bacterial pathogens, two positive for Giardia, four positive for virus and 11 conventionally negative. The NGS-based approach enabled detection of the same bacterial pathogens as the classical approach in 34 of the 38 conventionally positive bacterial samples, and predicted responsible pathogens in five of 11 conventionally negative samples. Overall, the NGS-based approach enabled pathogen detection comparable to the conventional diagnostics, and the approach has potential to be extended for detection of all pathogens. At present, however, this approach is too expensive and time-consuming for routine diagnostics.
sample derived from
SAMEA4350162
sample name
ERR1543996_bin.47_CONCOCT_v1.1_MAG
scientific_name
uncultured Firmicutes bacterium
sequencing method
Illumina MiSeq
taxonomic identity marker
multi-marker approach