gut_otu_table: Abundance table of gut microbiome.
In RADanalysis: Normalization and Study of Rank Abundance Distributions

Dethlefsen et al. 2008 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060280) have treated healthy individuals with the antibiotic Ciprofloxacin and monitored the states of the gut microbiome before the treatment, during the treatment, and some time after the treatment.

1	data(gut_otu_table)

A matrix with 18 rows and 5670 columns.

Abundance table of 18 gut samples from 3 individuals, prior, under and after using Ciprofloxacin (Cp) antibiotic. Each row is the abundance of gut microbiome for one sample. The row names are as follows:

A1, B1 and C1 are samples from individuals A, B and C 60 days prior using Cp.
A2a is the sample from individual A 6 days prior using Cp.
A2b is the sample from individual A 2 days prior using Cp.
A2c, B2 and C2 are samples from individuals A, B and C one day prior using Cp.
A3a is the sample from individual A 3 days after the first day of Cp administration.
A3b, B3 and C3 are the samples from individual A, B and C 5 days after the first day of Cp administration.
A4, B4 and C4 are the samples from individual A, B and C 33 days after the first day of Cp administration.
A5, B5 and C5 are the samples from individual A, B and C 180 days after the first day of Cp administration.

points 1 and 2 are considered pre-Cp, points 3 are considered under-Cp and point 4 and 5 are considered post-Cp.

Dethlefsen, Les, et al. "The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing." PLoS biol 6.11 (2008): e280.

RADanalysis documentation built on May 2, 2019, 6:13 a.m.