Individual difference in microbiome composition

General Discussion
1

Hi all,

I analyzed the microbiome sequencing data and got the results from each animal.
But the microbiome composition is different among each animal in the same group. (Individual differences).
How can I adjust that difference?

For example, Mice 1(Group A) / Firmicutes (%) : Pre-treatment : 70% -> 1day after treatment : 50% -> 3 day after treatment : 30% (Decreased until 3 days)

But Mice 2 (Group A) / Firmitues (%) : Pre-treatment : 60% -> 1day after treatment : 60% -> 3 day after treatment : 70%. (Increased until 3 days)

Both Mice 1 and 2 are involved in the Same group but they have a different trend.
Is there a good method to adjust that value? I don’t think the mean value of those Mice 1 and Mice 2 is the correct value.

Thanks.

Best,
JJ

2

Hi @Julie_Jeon,
Sounds like you have subject effects in a longitudinal experiment. Check out the methods in q2-longitudinal and the tutorial for that plugin on qiime2.org! The pairwise-* actions are designed for paired comparisons between two time points, e.g., in a pre-post experiment (which sounds like what you may have). For longer longitudinal studies, you could use linear-mixed-effects which in this plugin always uses an individual intercept to adjust for subject effects. See the tutorial for more details on all these actions.

Good luck!

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