minimalgut: Human Gut Minimal Microbiome Profiling Data

In microbiome/miaTime: Microbiome Time Series Analysis

Human Gut Minimal Microbiome Profiling Data

Description

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.

Usage

data(minimalgut)

Format

The data set in TreeSummarizedExperiment format.

Details

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.

Value

Loads the data set in R.

Author(s)

Sudarshan A. Shetty

References

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.

microbiome/miaTime documentation built on May 7, 2023, 2:06 p.m.