Antimicrobial resistome data analysis with R/Bioconductor

Team Leo Lahti University of Turku, Finland.

Team home page

Data Source

This large-scale study includes a total of 9,251 samples collected from various human body sites and countries.

Raw Illumina sequencing reads from NCBI or EMBL using Kingfisher-download
Metagenomic assemblies retrieved from the paper “Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle”

6104 adult gut metagenome samples from 20 countries after refinning
curatedMetagenomeData R package for retrieving the sample metadata

Manually curated ARG families from CARD database (n=752)

Sample Distribution by Body Site

The dataset comprises samples from six major body sites, with the distribution as follows:

Sample Distribution by Country

Data overview in R

TreeSummarizedExperiment

class: TreeSummarizedExperiment 
dim: 4182 5195 
metadata(1): Country
assays(1): relabundance
rownames(4182): 362 363 ... 23727 23733
rowData names(13): sgbid sgbname ... assigned_pathogen_name
  assigned_pathogen_taxid
colnames(5195): AsnicarF_2017__MV_FEM1_t1Q14
  AsnicarF_2017__MV_FEM2_t1Q14 ... ZellerG_2014__CCMD74930188ST-21-0
  ZellerG_2014__CCMD79987997ST-21-0
colData names(22): Tier_1.Exclusion_before_analysis
  Tier_2.Recover_all_40_SCGs ... antibiotic_exposure_status_descriptive
  antibiotic_current_use_binary
reducedDimNames(0):
mainExpName: NULL
altExpNames(2): read assembly
rowLinks: NULL
rowTree: NULL
colLinks: NULL
colTree: NULL