Multivariate Analysis for a paired subject longitudinal microbiome study

I am trying to finish my stats analyses for a microbiome study, and the last thing on my list is multivariate analysis. I have a paired group of infants and their primary caregivers with samples taken 5 times over a 1 year period along with clinical data (sex, feeding, delivery etc). I'm looking to see how the microbiome is affected by time throughout the year, infants vs caregivers, as well as feeding habits etc. I've been using R for my analysis and I've read some instruction manuals online, but nothing seems to cover my needs.