Difficulty interpreting the results of Permanova and Bray Curtis

General Discussion
,
1

Hi everyone :grinning:

Is anyone available to help me interpret and understand my beta diversity results? particularly Permanova and Bray Curtis.
I am analysing the gut microbiome of an insect species raised on a treated and a control diet and would like to see any bacterial community differences.
From the permanova test, I obtained a significant difference between the diets (p= 0.04) but looking at the Bray Curtis graph, I don't seem to notice any differences. Maybe I'm misinterpreting the graph;
could someone help me?

Thank you very much in advance

unweighted-unifrac-treatment-significance.qzv (308.7 KB)
bray_curtis_emperor.qzv (861.7 KB)

2

Hi!
Looks like you provided PERMANOVA results for unweighted unifrac and PCoA for Bray-Curtis, which are different metrics (you should use the same metric for both).
But on the PCoA plot you can easily distinct two groups of the samples based on the treatment - just draw a line from upper end of Axis2 to the right end of Axis1 and you see that samples can be divided by such line.

Hope it helps.

Best,

1 Like
3

Hi Timur!

Thank you so much for your help!
Unfortunately I don't understand very well how to distinct two groups with line.
Could you show me?

4

You don't need that line - it is a tool from my imagination...

But here it is

Screenshot from 2023-11-23 16-00-23
Screenshot from 2023-11-23 16-00-231732×1029 69 KB

On the right panel, one can adjust color, size, axes, shapes, and visibility to help with group differentiation.

2 Likes
5

thank you very very much!!
You were really a great help!
I also did the permanova on the bray curtis distance, was this what you meant before?
bray-curtis-treatment-significance.qzv (311.9 KB)

1 Like
6

Thank you for sharing!
In general, looks correct - you have 2 distinct groups on PCoA with a significant PERMANOVA test.

2 Likes