Hello Everyone! A big thanks for the Qiime Team and others who are contributing to the forum.
I have 16s data (feces) from an inbred panel of mice - I have 6 animals per line (3 males and 3 females) for about 25 lines. I am trying to answer the following questions
Is the microbiota different between the lines?
Ans : Beta diversity group significance - PERMANOVA results.
What are the major OTU’s that make them different?
Ans: ANCOM - the highest W values OTU’s
Are the animals within the same line have similar microbiota? (to make sure I have a homogenous line - feces was collected during various experiments and time through a period of 2 years )
problem: sample size of six
if I know the disease outcomes for these lines, can I predict which OTU’s contribute to resistance?
Ans: machine learning classifiers - which estimator to select?
If I am using the OTU’s to run some QTLs to see if there are genes associated with the microbiome? which level is appropriate for 16s data
Ans: Order, family, or genus?
Please add comments or additions to any of these steps or any additional steps which I should do?
Thanks in advance!