Hi all! I'm seeking your expert opinion on sample comparison in time series for 16S rRNA microbial analysis. I'm analyzing a gut microbiome to perform a time series analysis of their changes from early days post hatching until adulthood. I was given DNA sequences with one time point having DNA sequences from pooled DNA samples representing one biological replicate each while the other time points have individual sequence of each biological replicate (around 3 to 5 replicates each time point). Will it make sense for me to compare the sequences of pooled DNA samples with other time points whose data sets were not pooled, or it's not scientifically sound at all to pursue this analysis (e.g. compare the changes from early time points to late time points but one of the time points uses 16S sequences from pooled DNA samples while others are individual actual biological replicates, all these in one dataset analysis)? I'm planning to do both beta and alpha diversity analyses on these samples. Thanks a lot!
Previously, my posts have been dealing with a lot of sampling and replicates issues which I have no control of and that's why I'm seeking again help because this is beyond my knowledge and the last thing I wanna do is to assume or guess in areas that I don't have deep knowledge. I'm dealing with this another sample problem again from a different set of data hoping there's something that I could work on for these data. This community has always been helpful and thankful for all the kind and insightful responses. Thank you very much and regards.
