We want to investigate if certain treatment (nutrition supplement) changes mouse fecal microbiome, and if it does then how long does it take to change the biome? We have sample from -3 days to 21 days (every alternate day collection). We will be doing 16 S rRNA gene seq/MiSeq. What I am not sure is how best to use 96 indexes? That is to say whether to:
1. take 3 mice (individually indexed) per day per treatment and do more samples over 21 days or
2. take 5 mice (individually indexed) per day per treatment and do samples but from intermittent days.
Your comments / critique welcome!
1. take 3 mice (individually indexed) per day per treatment and do more samples over 21 days or
2. take 5 mice (individually indexed) per day per treatment and do samples but from intermittent days.
Your comments / critique welcome!
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