Nature has published a comment by William P. Hanage suggesting ways to inoculate oneself against the hype associated with the burgeoning field of microbiome studies. As Bethany Brookshire (aka, SciCurious) notes, these questions should be applied to any and all research, not just the microbiome.
1. Can experiments distinguish differences that matter?
2. Does the study show causation or just correlation?
3. What is the mechanism?
4. How much do experiments reflect reality?
5. Could anything else explain the results?
–paraphrased from William P. Hanage in Nature
The Finch and Pea 