2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21067258
SRA accession
spire_mag_02346119
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
not provided
collection date
93.86
%
completeness score
checkm2 0.1.3
completeness software
0.28
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR13348730 of study SRP300203.
description
stool
environmental medium
Tanzania
geographic location (country and/or sea)
missing: third party data
DD
geographic location (latitude)
missing: third party data
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
The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Stool metagenomics uncovers a gradient of intestinal microbial compositions from rural through urban Tanzania, towards European samples, manifested both in relative abundance and genomic variation. The rural population shows increase Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 significant microbes. Pathway effects on cytokines, notably TNF-alpha and IFN-gamma, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.
project name
SAMN17126991
sample derived from
Bacteroides uniformis
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02346119
title