Hi; It is not recommended using WGCNA on less than 20 individuals. My question is what is the exact meaning of individuals? I have 7 bacterial colonies and three replicates for each one. Now i have 7 individuals or 21? Also i want to know is it recommended to use this package between subspecies?

The recommendation is 20 samples rather than individuals. You can run WGCNA on the 21 samples as an exploratory analysis; just be aware that any association p-values you observe between say modules and traits may not be accurate.

My experience with bacterial/subspecies data is zero so consider my answer in the "for what it's worth" category, but if the subspecies are not very different from one another in terms of their genetic makeup, WGCNA should make sense.