From the article: "The microbiome field is negotiating the same cycle of hype, backlash, and introspection [other preliminary medical findings have experienced]. Thousands of studies have linked the microbiome to almost every condition you can imagine, but many of these correlations are likely to be illusory. 'A lot of people have been annoyed by the hype surrounding our area, and I think they were probably right,' says Raes. 'It’s time that, from within the field, we look critically at what we’re doing ourselves. We tried to do that with our paper. Yes, we’ve had the hype. Now, it’s time for the consolidation.'"
Here on Hacker News, I have seen repeated articles become greeted by comments that assume we already know all about how to regulate what microbes are in our guts and how that influences health. In fact, we have no idea about such things and don't have nearly enough data yet to make any definite statements about how gut microbes really to human health, or even if they influence human health at all for most people.