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Metagenome-assembled genome: ERR1620353_bin.79_CONCOCT_v1.1_MAG

Identifiers
BioSample: SAMEA14083849; SRA: ERS11686983
Organism
uncultured Veillonella sp.
cellular organisms; Bacteria; Bacillati; Bacillota; Negativicutes; Veillonellales; Veillonellaceae; Veillonella; environmental samples
Attributes
collection date2013-01-01
broad-scale environmental contextHost-associated
local-scale environmental contextHuman
environmental mediumDigestive system
geographic locationChina
investigation typemetagenome-assembled genome
isolation sourcehuman gut metagenome
project nameAbstractBackgroundInflammatory bowel diseases (IBD), with Crohn’s disease (CD) being one of the primary types, have been extensively studied for genetic and gut microbial factors leading to its epidemic in the modern world. However, limited information using metagenomic shotgun-sequencing to pinpoint the gut microbial species and functions involved. Exclusive enteral nutrition (EEN) is a nutritional therapy used for disease-modifying treatment of CD, but its impact on the gut microbiome remains unclear. ResultsWe collected 123 stool samples from 49 CD patients, 14 of whom were resampled after 2 weeks of EEN, and 56 subjects with no disease. Metagenomic shotgun sequencing and analyses confirmed a decreased diversity in the gut microbiota of CD patients, and identified microbial species and potential functions altered in CD, most notably an increased ratio of hexa- to penta-acylated lipopolysaccharide (LPS). Some co-abundance gene groups (CAGs) including Parabacteroides distasonis, Bacteroides intestinalis, Ruminococcus sp. showed strong correlation with clinical indicators such as hs.CRP, Prealbumin, platelets and BMI. The entire cohort could be divided into three types according to their species composition, with Type A largely consisting of healthy controls and Type C containing exclusively CD or after EEN samples. Although compositional changes were generally mild after 2 weeks of EEN, remodeling of the gut microbial network could be observed.ConclusionsOur metagenomic dataset unlock the gut microbiome in CD for functional investigations. Microbiome-based stratification of CD patients before EEN might help optimize the therapy for wider applications.
sample nameERR1620353_bin.79_CONCOCT_v1.1_MAG
ENA-CHECKLISTERC000047
ENA-FIRST-PUBLIC2023-01-03
ENA-LAST-UPDATE2023-01-03
External IdSAMEA14083849
INSDC center aliasEBI
INSDC center nameEuropean Bioinformatics Institute
INSDC first public2023-01-03T00:33:12Z
INSDC last update2023-01-03T00:33:12Z
INSDC statuspublic
Submitter IdERR1620353_bin.79_CONCOCT_v1.1_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspadesv3.11.1
binning parametersDefault
binning softwareCONCOCT v1.1
broker nameEMG broker account, EMBL-EBI
completeness score93.18
completeness softwareCheckM
contamination score2.11
geographic location (latitude)55.676098
geographic location (longitude)12.568337
metagenomic sourcehuman gut metagenome
sample derived fromSAMEA4431966
scientific_nameuncultured Veillonella 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 ERR1620353 of study ERP017091.

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:
SAMEA14083849
ID:
32560478

BioProject Nucleotide

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