2024-09-20
ENA first public
ERC000050
ENA-CHECKLIST
EMBL Heidelberg
INSDC center name
public
INSDC status
ERS21064327
SRA accession
spire_mag_02394499
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
collection date
66.7
%
completeness score
checkm2 0.1.3
completeness software
0.12
%
contamination score
This sample represents a Third Party Annotation (TPA) binned metagenome assembled from the metagenomic run SRR13789222 of study SRP306763.
description
stool
environmental medium
USA
geographic location (country and/or sea)
41.73000000
DD
geographic location (latitude)
-72.79000000
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
While older adults represent a vulnerable population with elevated risk for numerous chronic illnesses, the role played by the microbiome in such age-related susceptibilities remains largely unexplored. Stereotypical changes in physiological and immune responses with aging likely contribute to microbiome-related increases in predisposition to common late life diseases. To understand associations of the microbiome with age, frailty, and infectious disease risk factors, we conducted a longitudinal, whole genome shotgun study of the skin, oral, and gut microbiota in 47 older adults residing in community or skilled nursing facility (SNF) settings. We found prominent differences in microbiomes from all body sites between younger adults, older adults living in the community, and SNF residents. In addition, frailty correlated negatively with relative abundance of Cutibacterium (C.) acnes in the skin microbiome, which itself strongly correlated with decreased microbial community stability and increased diversity, heterogeneity, and biogeographic determinism, factors that have been associated with susceptibility to pathogen colonization and disease risk. Strikingly, the skin microbiota, rather than gut or oral communities, was the primary reservoir for plasmid-borne antimicrobial resistance and clinically important pathobionts. Strain composition of important commensal species such as C. acnes and Staphylococcus epidermidis in SNF residents further suggested a shift from healthy to pro-inflammatory and nosocomial strains. Our findings set the foundation for understanding relative risk of microbiome-mediated frailty and disease processes in older adults in different residential settings, and for the development of strategies to leverage the microbiota as tools to promote healthy aging, disease prevention, and to limit the dissemination of multidrug resistant pathogens.
project name
SAMN17617614
sample derived from
Phocaeicola vulgatus
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
binned metagenome: spire_mag_02394499
title