I am performing alpha beta diversity analysis (UniFrac plot) but when I view it, I see "axis 1," "axis 2," and "axis 3" and samples are spread out on these axis. What are these axis telling us? I have no clue. Please help me to understand what this graph is telling me using the moving-tutorials example if possible. Also, axis 3 means 3 dimensions but I only see a 2-D graph. I am confused!
Also, my supervisor wants me to figure out how many bacterial species are present in the water samples and how many reads correspond to each bacterial species? What is the best QIIME tool to get this kind of information for microbiome analysis?
This is an interactive plot. You can use your cursor/mouse to drag the plot around and view the 3 dimensions from different angles. There is a panel on the right side of the screen that allows you do adjust different values for color, shape, the dimensions, etc. See this tutorial for more details (though note that not all features described on that tutorial may be accessible in QIIME2).
That is alpha diversity. Follow the moving pictures tutorial for alpha diversity to learn how to do this analysis. To specifically perform this analysis as it pertains to species, use taxa collapse to collapse a feature table based on the taxonomy assigned — this process is described at the end of the moving pictures tutorial. To count the number of species observed in each sample, perform alpha diversity analyses on the collapsed feature table. You can then use qiime feature-table summarize to summarize that feature table and look at the total number of sequences that belong to each taxon.