How I can read the Axis 1 (14.7%) and Axis 2 (28.3%) on a PCoA plot for understanding beta diversity of gut microbiome?

I am particularly stuck in understanding the percent values and want to learn how to interpret the percent values? In other words, what does 14.7% and 28.3% mean in terms of beta diversity?

Hello Samiullah,

Welcome to the forums!

Axis 1 and 2 are Principal Coordinates 1 and 2. The percentages are (usually) the percent of total variation explained by that axis. So the separation of you see on Axis 1 is 14.7% (or 0.147/1.0) of the total variation in the distance matrix.

Principal Coordinate 1 usually explains the most variation, so having Axis 2 have a higher number is a little strange to me...

Would you like to post your script and PCoA plot so we can confirm?

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