U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Metagenome-assembled genome: ERR479355_bin.20_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14084436; SRA: ERS11687569
Organism
uncultured Prevotella sp.
cellular organisms; Bacteria; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella; environmental samples
Attributes
collection date2004-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationFrance
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameSeveral bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved >45% relative to the FOBT while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early and late-stage cancer and could be validated in independent patient and control populations (N=335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients accompanied by an increase of lipopolysaccharide metabolism.
sample nameERR479355_bin.20_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14084436
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:36Z
INSDC last update2023-01-03T00:33:36Z
INSDC statuspublic
Submitter IdERR479355_bin.20_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes v3.14.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score93.64
completeness softwareCheckM
contamination score2.45
geographic location (latitude)0.0
geographic location (longitude)0.0
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA2466934
scientific_nameuncultured Prevotella sp.
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 ERR479355 of study ERP005534.

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:
SAMEA14084436
ID:
32561064

BioProject Nucleotide

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center