An example gut microbiome dataset derived from the
curatedMetagenomicData HMP_2019_ibdmdb resource (iHMP/HMP2 IBD
cohort; Lloyd-Price et al., 2019).
The object is provided as a
TreeSummarizedExperiment.
The dataset contains 44 stool samples (two time points per subject: baseline
T0 and follow-up T1) from 22 subjects with inflammatory bowel
disease, with 585 microbial species.
Assays include relative abundance (relabundance) and a scaled version
of the same data (scaled). Taxonomic annotation is stored in
rowData, and a phylogenetic tree is available via rowTree.
Sample metadata (colData) includes subject identifiers, time point,
IBD subtype (CD/UC), and additional technical and demographic variables.
data(HMP_2019_ibdmdb)The data set in
TreeSummarizedExperiment
format: 585 microbial species (rows) and 44 stool samples (columns).
Derived from curatedMetagenomicData (Lloyd-Price et al., 2019).
Loads the data set in R.
Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. (2019). Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662. doi:10.1038/s41586-019-1237-9