I conducted an experiment with 20 newborn calves and I analyzed tissue samples collected in the colon at birth (baseline) and at d5 of life in the same animals. I have 2 groups of calves CON and TRT (treatment started just after first sample collection) and I would like to look at the time and TRT effects on microbial population. I also have the gene expression in the same samples and would like to find the best tool to look at the correlation between host and microbial populations.
I was thinking at ANCOM and Sparcc analysis, do you have any other suggestions?
Concerning the ANCOM analysis, what is the best way to run it? Can I use the d0 as a baseline and look at the differences concerning the treatment AND the time? Or should I split my dataset?
Many thanks in advance,