A subset of the gnotobiotic mouse gut microbiome experiment of Patnode et al. (2019), used for the real-data illustration in the paper. Gnotobiotic mice colonised with a defined 15-member human gut bacterial consortium were fed a high-saturated-fat/low-fruit-and-vegetable (HiSF) diet supplemented with different fibres, and the community was profiled at day 12. Two categorical covariates are recorded: diet (three levels: HiSF control, 10% citrus pectin (CPT), 10% pea fibre (PEF)) and the presence/absence of Bacteroides cellulosilyticus WH2 (OTU 2).
Format
A list with elements:
- Y
A
69 x 15integer matrix of OTU counts (samples in rows).- Xmean
A
69 x 5design matrix for the mean regression.- Xcov
A
69 x 4design matrix for the covariance regression (first column is the intercept).- species
A length-15 character vector mapping OTU columns to bacterial species.
Source
Patnode, M. L. et al. (2019). Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell 179(1), 59-73.