This time-series data set contains absolute temporal abundances for 16 human gut species that were assembled in an in vitro gut system. These were subjected to a variety of disturbances over a period of 20 days. The sample data includes measurements for Acetate, Butyrate, Propionate, and optical density.
data(minimalgut)The data set in
TreeSummarizedExperiment
format.
Loads the data set in R.
The data is available also on
https://github.com/microsud/syncomR
The data contains 183 samples from 3 in vitro gut system, 61 per bioreactor
collected three times daily.
The current implementation in miaTime provides this as
TreeSummarizedExperiment
object.
Shetty, S.A., Kostopoulos, I., Geerlings, S.Y. et al. Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. ISME, 16, 2144–2159 (2022). https://doi.org/10.1038/s41396-022-01255-2.