data-enterotype: (Data) Enterotypes of the human gut microbiome (2011)

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

Published in Nature in early 2011, this work compared (among other things), the faecal microbial communities from 22 subjects using complete shotgun DNA sequencing. Authors further compared these microbial communities with the faecal communities of subjects from other studies. A total of 280 faecal samples / subjects are represented in this dataset, and 553 genera. The authors claim 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, but with potential relevance to understanding human gut microbiota.

Details

abstract from research article (quoted):

Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.

(end quote)

Author(s)

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

References

Arumugam, M., et al. (2011). Enterotypes of the human gut microbiome.

Nature, 473(7346), 174-180.

http://www.nature.com/doifinder/10.1038/nature09944 See supplemental information for subject data.

OTU-clustered data was downloaded from the publicly-accessible:

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

Examples

data(enterotype)
ig <- make_network(enterotype, "samples", max.dist=0.3)
plot_network(ig, enterotype, color="SeqTech", shape="Enterotype", line_weight=0.3, label=NULL)

Example output

Warning message:
attributes are not identical across measure variables; they will be dropped 

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.