Hi, I am planning to perform amplicon-based sequencing (16s and fungal ITS) of microbiome analysis of multiple samples from a specific niche. I have some experience with the analysis part of the study which follows the sequencing step, as I have done quite a few practice analyses of published sequence data. But my next study involves actual sample collection and handling, which is a first for me. And have a few questions that I hope someone can help me with to be better prepared -
- Anyone with experience in this, what are some unexpected hurdles that you had to overcome during your first few studies?
- Having a “mock” synthetic community among your samples- Is it necessary? What benefits does it offer? I understand it can help identify errors during the analysis pipeline.
- What is the ideal composition of a mock community? Should the microbial compositions be broad and cover all possible branches? Or should it be composed of organisms likely to be found in the niche under study?
Apologies if this is not the right forum for this question, but I could not find a better forum of experienced users regarding this