7 What Next?

What you have learnt so far is just the beginging!! There is a lot more ot learn and do.

For example, after looking at beta diversity, you can also look at differential abundance to see which taxa are different in each treatment group or over time.

Most commonly used methods for doing this is deseq2 and a new one is corncob. Before using them, please read the papers carefully to know the limitations and correct usage of these pacakages.

Some people also try to do functional analaysis with 16s data and for this PICRUST2 pacakge is usually used.