In the same study, fungi OTUs are analyzed by species, bacteria OTUs by genus. This is what the data looks like, and we can not re-analysis it. Does that make scientific sense and common in microbiome study? Are there pitfalls we should be aware of when analyzing them？
Thank for your help!
Hello @Wang_cs001632,
Welcome to the forums! 
I'm not sure if using different taxonomy levels for fungi and bacteria in the same study is common, but can be done. When I worked on this paper, we chose to use Phylum for bacteria and Class for Eukaryotes in Figure 4, because we though these taxonomy levels were most useful, even though they were different.
Most of our analysis in that paper takes place at the feature level, so Phylum vs Class does not matter.
I would want to know why the authors chose to use different levels, and that will tell you what pitfalls you can expect. They are using different levels to solve a problem, so I want to know about the problem they are trying to solve with mismatched taxonomy levels, and if using mismatched levels creates new problems.
Colin
P.S.
If the paper is already published, the data should be too, and re-analysis should be possible if it's really really needed! But that takes more time and money! 
P.P.S.
Happy New Year!
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