2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21063547
SRA accession
spire_mag_02010818
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
2016
collection date
97.45
%
completeness score
checkm2 0.1.3
completeness software
0.25
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run ERR2840888 of study ERP110930.
description
stool
environmental medium
USA
geographic location (country and/or sea)
44.97780000
DD
geographic location (latitude)
-93.26500000
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
human gut metagenome
isolation_source
human gut
local environmental context
human gut metagenome
metagenomic source
Phocaeicola vulgatus
organism
Many United States immigrant populations develop metabolic diseases post-immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of U.S. immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the U.S., including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 U.S.-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the U.S. is associated with immediate loss of gut microbiome diversity and function, in which U.S.-associated strains and functions displace native strains and functions. These effects increase with duration of U.S. residence, and are compounded by obesity and across generations.
project name
SAMEA4973145
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02010818
title