microcosm: Cow microbiome data set

Description

This data gives the evolution of the microbiota of 45 lactating cows before and after calving in terms of counts of Amplicon Sequence Variants (ASV) in various body sites. Three body sites (vagina, mouth, nose) in addition to the milk of the 4 teats were sampled at 4 times points: 1 week before calving (except for the milk), 1 month, 3 months and 7 months after calving. We present a reduced version of the original data consisting of 880 samples with sequencing depths ranging from 1,001 to 71,881 reads per sample (see tools:::Rd_expr_doi("10.1186/s42523-023-00252-w") for details). ASVs with prevalence in the dataset lower than 5% were filtered out and samples for which the total depth (after ASV filtering were removed), resulting in a count table of n = 880 samples with p = 259 ASV and a mean proportion of zeroes of 90.3%.

Usage

microcosm

Arguments

Format

A data frame with 6 variables:

Abundance: A 880 samples by 259 taxa count matrix
sample: Unique sample id
Offset: sequencing depth
site: sampling site (O: oral; N: nasal; V: vaginal; M: milk)
time: sampling time (-1W: 1 week before calving; 1M: 1 month after calving; 3M: 3 months after calving; 7M: 7 months after calving)
site_time: factor of possible pairs of (site, time). The combination M -1W is absent.

References

Mariadassou, M., Nouvel, L.X., Constant, F. et al. Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd. anim microbiome 5, 32 (2023). tools:::Rd_expr_doi("10.1186/s42523-023-00252-w")

Examples

Run this code

data(microcosm)
if (FALSE) {
my_ZIPLN <- ZIPLN(formula = Abundance ~ 0 + site + offset(log(Offset)) | 1, data = microcosm)
}