The firstt thing to keep in mind is that tutorial datasets are designed to be easy! It’s one fo the weird keys in picking/working with tutorial data. So, it doesn’t surprise me that you’re not seeing clear clustering. Frankly, if I see that much clustering normally in my samples, I worry about technical effects rather than real biological signaling.
There are a couple approaches I might consider. I’ve been using Adonis a lot recently to get a sense of relative effect sizes with metadata. This can kind of help you screen. You can also visualize with boxplots (beta-group-significance) to give you a sense of comparison.
I would suggest taking your data outside of QIIME for an area plot. R, Excel, python, stata(?), crayon () … pick your poison. It’s still very descriptive, but its there.
“There is no difference” is a valid answer to an experiment if you’ve been rigerous. (So is “not enough data”).