2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21067032
SRA accession
spire_mag_02233333
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
2018-01-01/2019-08-01
collection date
54.97
%
completeness score
checkm2 0.1.3
completeness software
1.74
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR12557710 of study SRP219080.
description
stool
environmental medium
Mexico
geographic location (country and/or sea)
23.63000000
DD
geographic location (latitude)
-102.55000000
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
Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. In this study, we performed the first large-scale de novo assembly of microbial genomes from paleofeces. From eight authenticated human paleofeces (1,000-2,000 years old) with well-preserved DNA from the Southwestern U.S. and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent novel species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. Compared to 789 present-day human gut microbiome samples from eight countries, the paleofeces are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the paleofeces reveals significantly lower abundance of antibiotic resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This work opens the door to discovering and characterizing novel gut microbes from ancient microbiomes and interrogating the evolutionary history of the human gut microbiota through genome reconstruction from paleofeces.
project name
SAMN12619405
sample derived from
Bacteroides uniformis
scientific_name
Illumina HiSeq 4000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02233333
title