binned metagenome: spire_mag_02233432
Bacteroides uniformis
ENA first public
2024-09-20
INSDC center name
EMBL Heidelberg
INSDC status
public
Submitter Id
spire_mag_02233432
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
2018-01-01/2019-08-01
completeness score
91.27
completeness software
checkm2 0.1.3
contamination score
5.37
environmental medium
stool
geographic location (country and/or sea)
Mexico
geographic location (latitude)
23.63000000
geographic location (longitude)
-102.55000000
investigation type
metagenome-assembled genome
isolation_source
human gut metagenome
local environmental context
human gut
metagenomic source
human gut metagenome
project name
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.
sample derived from
SAMN12619395
sample name
spire_mag_02233432
scientific_name
Bacteroides uniformis
sequencing method
Illumina HiSeq 4000
taxonomic identity marker
multi-marker approach