I have a question about pathway-level results.
Yannan Huang
I am Yannan from Dalhousie University. I am using PICRUSt2 to analyze wastewater and soil samples based on MiSeq 16S v6-v8 sequencing data.
I have a question about pathway-level results. I see that the nitrifier denitrification pathway (PWY-7084) is selected over other pathways like ammonia oxidation I (aerobic) or ammonia oxidation IV (autotrophic ammonia oxidizers). All five (EC:1.14.99.39, EC:1.7.2.6, EC:1.7.2.1, EC:1.7.2.5, EC:1.7.2.4) numbers are listed in the nitrifier denitrification pathway. I understand the nitrifier denitrification pathway is chosen. However, EC:1.14.99.39 and EC:1.7.2.6 are also listed in ammonia oxidation I (aerobic) or ammonia oxidation IV (autotrophic ammonia oxidizers) pathways. Those two pathways are not chosen. If you could help me understand why those two were not chosen, it would be greatly appreciated.
I have attached the files for your review.
I hope my question is clear, but please let me know if you need more information.
Thank you,
Yannan
Yannan Huang
Hi PICRUSt2 group,
After posting the first question last week, I have looked into more about how the pathway abundance is calculated. The PICRUSt2 uses the similar calculation as HUMAnN2 if I understand it correctly.
The pathway is selected over other pathways, is because reactions' abundances are equal to or above the harmonic mean of the reaction abundances depending on the relationships of these reactions involved in the pathway. Other pathways are not selected, because the reactions abundances are below the harmonic mean. Do I interpret correctly?
Thank you,