Is coffee bad for you or good for you? Does acupuncture actually work, or does it produce a placebo effect? Do kids with autism have different microbes living in their intestines, or are their gut flora largely the same as neurotypical children? These are all good examples of topics that have produced wildly conflicting results from one study to another. (Side-note: This is why knowing what a single study says about something doesn't actually tell you much. And, frankly, when you have a lot of conflicting results on anything, it's really easy for somebody to pick the five that support a given hypothesis and not tell you about the 10 that don't.)
But why do conflicting results happen? One big factor is experimental design. Turns out, there's more than one way to study the same thing. How you set up an experiment can have a big effect on the outcome. And if lots of people are using different experimental designs, it becomes difficult to accurately compare their results. At the Wonderland blog, Emily Anthes has an excellent piece about this problem, using the aforementioned research on gut flora in kids with autism as an example.
For instance, in studies of autism and microbes, investigators must decide what kind of control group they want to use. Some scientists have chosen to compare the guts of autistic kids to those of their neurotypical siblings while others have used unrelated children as controls. This choice of control group can influence the strength of the effect that researchers find–or whether they find one at all.
Scientists also know that antibiotics can have profound and long-lasting effects on our microbiomes, so they agree on the need to exclude children from these studies who have taken antibiotics recently. But what's recently? Within the last week? Month? Three months? Each investigator has to make his or her own call when designing a study.
Then there's the matter of how researchers collect their bacterial samples. Are they studying fecal samples? Or taking samples from inside the intestines themselves? The bacterial communities may differ in samples taken from different places.