Core microbiome % error?


I used the core microbiome within the microbiome analyst and do not get detection thresholds over 1%. But within the data there are multiple ASVs with relative abundances of 1% and more.

I would suspect that there is no calculation to % (0 to 100) but only relative abundance (0 to 1)?
For example, OTU00005 (bottom of ASV table) should have a prevalence of 1 at 0.01 relative abundance % but is only at around 0.5 according to the color code.

ASV_microbiomeanalyst_small.csv (298.1 KB)
META_microbiomeanalyst_small.csv (979 Bytes)
TAX_microbiomeanalyst.csv (1.3 MB)

Cheers, Tobias

Hello, the relative abundance in the core microbiome analysis is used to set the threshold of the relative abundance of the feature in a sample. The prevalence calculate the percentage of the samples in which the relative abundance of the given feature is over the threshold. For instance, the prevalence 0.5 of OTU00005 means that the relative abundance of OTU00005 is more than 0.01 in ~50% samples.

Hope this helps!


thank you for pointing out how the prevalence is calculated, I was wondering about how that works.

But that still leaves the question why there is no OTU detected in the core microbiome if the relative abundance threshold is at 1% or above. Because OTU00005 clearly has relative abundances of 1% and above (reaching up to 12%).
With the settings:
Sample threshold 10%
Relative abundance threshold 1%
I should at least get OTU00005 in the plot but I only get this error message:
Error No core features were detected using the current prevalence and relative abundance thresholds.

Thank you in advance!

Hello, I have performed the core microbiome analysis with the threshold you have set and it works properly as shown:

Could you please try again and let us know if you still get the error? If so, please provide more details. Hope this helps!

yeah it works with a relative abundance of 0.01 but with 1 it gives me an error:

And it has an abundance above 1% in some samples.
Thank you!

Hello, this might not be an error but just because there was no features passed the filtration. You can check if it is reasonable for your data.

That is the problem here, following are the relative abundances of OTU00005 in %:

6.572539545 1.89957952 4.43130232 4.651009975 1.169973793 9.787746779 12.29950018 0.394600208 0.870634367 1.234822688 0.116913484 0.191777538 0.07349853 0.062271347 0.090734415

So it would be reasonable to have atleast OTU00005 appear in the 1% filter (and should also have a 100% prevalence with your settings).

Sorry to keep bothering and thank you very much!