Hello,
We perform 16S analysis on samples collected from chickens and pigs from all over the world. Although these animals belong to the same species and share similar dietary habits, is it normal to observe different Shannon entropy values among them?
Typically, I see that Shannon entropy values range from 2 to 5 in publications but in my analyses, I sometimes encounter values between 7 and 10. Recently, our NEW sequencing platform provided separate fastq.gz files accompanied by a report mentioning entropy values ranging from 3 to 6. However, after running my pipeline—which includes quality checking, denoising, and taxonomic assignment. I observe Shannon entropy values between 6 and 8.
Could this discrepancy be considered normal? Is it possible that this difference arises from using different tools or methods to calculate the Shannon entropy? I believe our sequencing platform uses SNAP version 1.0.23.
Most likely yes. Shannon entropy can be calculated with different logarithmic bases, and different tools will use different bases by default, which can lead to such a discrepancy when comparing estimates from different tools, or when comparing to literature.
Many other things will also impact the discrepancy in literature, e.g., different sequencing technologies, molecular targets, etc.
There is a little more discussion of this in this topic, I suggest reading there for more details:
thank you!! first question
you said that "The Shannon index uses a log scale, but it can use log2 or log10 or natural log, and all of these are perfectly valid nobody EVER reports which one they are using!" what qiime2 apply in this case ? second quesiton:
Can the animal species and the country where it is raised affect the values?