Bacteroides uniformis
ENA first public
2024-09-21
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_01477290
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
megahit 1.2.9
binning parameters
default
binning software
metabat 2.12.1
broad-scale environmental context
human digestive system
broker name
EBI-EMG
collection date
2010-01-01
completeness score
51.7
completeness software
checkm2 0.1.3
contamination score
0.18
environmental medium
stool
geographic location (country and/or sea)
USA
geographic location (latitude)
42.44851
geographic location (longitude)
-76.47862
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
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.
sample derived from
SAMEA4731529
sample name
spire_mag_01477290
scientific_name
Bacteroides uniformis
sequencing method
Illumina HiSeq 3000
taxonomic identity marker
multi-marker approach