Please note, these scripts are purely intended as a descriptive extension of the methods used in the publication:
Aimée Parker, Stefano Romano, Rebecca Ansorge, Asmaa Aboelnour, Gwenaelle Le Gall, George M. Savva, Matthew G. Pontifex, Andrea Telatin, David Baker, Emily Jones, David Vauzour, Steven Rudder, L. Ashley Blackshaw, Glen Jeffery & Simon R. Carding, "Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain." Microbiome 10, 68 (2022). https://doi.org/10.1186/s40168-022-01243-w
If you wish to use any material in this repository please be aware that this code was tailored to the analyses conducted in the above manuscript and it is presented here to foster reproducibility. The code is not intended to be used in other contexts
The scripts are divided in 3 folders, containing the code for the analyses performed for the taxonomy, functional profiles, and metabolomics data. Scripts are numbered and have been executed sequentially.
If you find this code useful or use any of the approaches below in your work, please cite:
Parker, A., Romano, S., Ansorge, R. et al. "Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain." Microbiome 10, 68 (2022). https://doi.org/10.1186/s40168-022-01243-w
01 – Load data and perform alpha and beta diversity analyses
02 – Filter the data to perform differential abundance analysis at the species level
03 – Differential abundance analysis based on linear mixed models performed at the species level
04 - Differential abundance analysis based on linear mixed models performed at the species level to compare mice groups at the beginning of the experiment
05 – Filter the data to perform differential abundance analysis at the family level
06 – Differential abundance analysis based on linear mixed models performed at the family level
01 – Load the data and format them
02 – Differential abundance analysis based on linear mixed models
01 – Load data, format and transform them
02 – Perform ordinations and PLS-DA