How much does the DNA extraction route impact the results of microbiome research?

Let's face it, we are a results-driven society. Too focused on the outcome, people don't often think about the "how." For instance, did you think about "how" you got to work this morning or did you just get there? In microbiome studies the results are the graphs and the data but the "how," like commuting, is often just part of a routine.