2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21062112
SRA accession
spire_mag_01474569
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
2010-01-01
collection date
96.5
%
completeness score
checkm2 0.1.3
completeness software
1.5
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic runs ERR2641650,ERR2641321,ERR2641285,ERR2641790,ERR2641620 of study ERP109376.
description
stool
environmental medium
USA
geographic location (country and/or sea)
42.44851
DD
geographic location (latitude)
-76.47862
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
Human genetic variation influences the composition of the gut microbiome. Studies have focused on associations between components of the microbiome and single nucleotide polymorphisms in genes, but their copy number (CN) can also vary. Here, we relate oral and gut microbiome to CN variation at the AMY1 locus, encoding the salivary amylase gene active in starch degradation, in a study of human subjects including a 2-week standard diet. We show that diet standardization drove gut microbiome convergence, yet AMY1-CN influenced oral and gut microbiome composition and function. Low-AMY1-subject gut microbiomes showed an enhanced capacity for breakdown of complex carbohydrates, and high-AMY1 an enrichment of microbiota linked to resistant starch fermentation. High-AMY1-subject microbiomes were associated with higher fecal SCFAs, and drove higher adiposity when transferred to germfree mice. This study establishes AMY1-CN as a significant genetic factor patterning microbiome composition and function, with implications for personalized nutrition targeting microbiomes.
project name
SAMEA4731489
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina HiSeq 3000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_01474569
title