farmm: Food And Resulting Microbial Metabolites (FARMM) study data

In ctanes/miscStats: Bonus material for the adonis function

Food And Resulting Microbial Metabolites (FARMM) study data

Description

Information on samples collected in the FARMM study, and a distance matrix containing Bray-Curtis distances between the microbial communities in each sample.

Usage

farmm_samples

farmm_bc

Format

farmm_samples is a data frame with 414 rows and 11 variables:

sample_id

unique identifiers for each sample, to match the distances in farmm_bc

subject_id

unique identifiers for each subject in the study

study_day

the day of the study on which the sample was collected

diet

the diet assigned to each subject

antibiotics

the antibiotics status of each subject during the study. A factor with three levels: "pre" (before antibiotic exposure), "current" (during antibiotic exposure), and "post" (after antibiotic exposure)

height

the height of each subject

weight

the weight of each subject

age

the age of each subject

bacterial_16S_copies

the number of bacterial 16S rRNA gene copies per gram feces, giving an estimate of absolute bacterial abundance

num_reads

the number of high-quality, non-host sequencing reads per sample

host_frac

the fraction of host reads in the shotgun metagenomic DNA sequencing data

farmm_bc is a dist object containing the Bray-Curtis distances between the 414 samples listed in farmm_samples.

Source

https://pubmed.ncbi.nlm.nih.gov/33440171/

References

Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021 Mar 10;29(3):394-407.e5. doi: 10.1016/j.chom.2020.12.012. Epub 2021 Jan 12. PMID: 33440171; PMCID: PMC8022197.

ctanes/miscStats documentation built on Nov. 24, 2024, 1:38 p.m.