I am doing rumen microbiome analysis. And I would like to extract rumen fluid from cattle to do in vitro analysis. For rumen fluid collected from each of the cattle, I would like do compare the effect of treatment to the microbiome profiles and fermentation characteristics using in vitro culture. So I think rumen fluid from different cattle can be considered as biological replicates. For chemical data, I can simply average the technical replicates. My question is how do I deal with the technical replicates for microbiome data? Should I compare the similarity of the sample and choose only one of the replicates or should I merge them? or can I simply combine the DNA from each replicates as one sample for sequencing?
I have came across this post, however, they were talking about simply sequence the same sample for multiple times while in my case, the samples are actually from different replicates.