enterotype: enterotype

In microbiome/mia: Microbiome analysis

enterotype

Description

The enterotype data of the human gut microbiome includes taxonomic profiling for 280 fecal samples from 22 subjects based on shotgun DNA sequencing. The authors claimed that the data naturally clumps into three community-level clusters, or "enterotypes", that are not immediately explained by sequencing technology or demographic features of the subjects. In a later addendum from 2014 the authors stated that enterotypes should not be seen as discrete clusters, but as a way of stratifying samples to reduce complexity. It was converted into a TreeSummarizedExperiment from the phyloseq package.

Usage

data(enterotype)

Format

A TreeSummarizedExperiment with 553 features and 280 samples. The rowData contains taxonomic information at Genus level. The colData includes:

Enterotype

enterotype the sample belongs to (1, 2 and 3)

Sample_ID

sample ID of samples from all studies

SeqTech

sequencing technology

SampleID

sample ID of complete samples

Project

original project from which sample was obtained (gill06, turnbaugh09, MetaHIT, MicroObes, MicroAge and kurokawa07)

Nationality

participant's nationality (american, danish, spanish, french, italian and japanese)

Gender

participant's gender (F or M)

Age

participant's age (0.25 – 87)

ClinicalStatus

participant's clinical status (healthy, obese, CD, UC and elderly)

Author(s)

Arumugam, M., Raes, J., et al.

Source

http://www.bork.embl.de/Docu/Arumugam_et_al_2011/downloads.html

References

Arumugam, M., et al. (2011). Enterotypes of the human gut microbiome. Nature, 473(7346), 174-180. https://doi.org/10.1038/nature09944

Arumugam, M., et al. (2014). Addendum: Enterotypes of the human gut microbiome. Nature 506, 516 (2014). https://doi.org/10.1038/nature13075

See Also

mia-datasets

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.