2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21070502
SRA accession
spire_mag_01979014
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
megahit 1.2.9
assembly software
default
binning parameters
metabat 2.12.1
binning software
human digestive system
broad-scale environmental context
EBI-EMG
broker name
2013
collection date
95.31
%
completeness score
checkm2 0.1.3
completeness software
0.47
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR1620280 of study ERP017091.
description
stool
environmental medium
China
geographic location (country and/or sea)
55.67609700
DD
geographic location (latitude)
12.56833700
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Bacteroides uniformis
organism
AbstractBackgroundInflammatory 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.
project name
SAMEA4431893
sample derived from
Bacteroides uniformis
scientific_name
Illumina HiSeq 2000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01979014
title