> Changes in faecal microbiota have been associated with a range of diseases in humans. Interestingly, despite the diverse nature of these conditions, and the organs they affect, there are some broadly common recurring microbiota features, such as reduced diversity and increases in facultative anaerobes like Enterobacteriaceae. One common theme amongst these conditions is that they often result in increased levels of inflammation, at local and systemic levels. Such inflammation can, in turn, deplete the gut microbiota (and consequently microbial gene diversity), and allow facultative anaerobes such as Enterobacteriaceae to proliferate. This directly impacts the metabolic output of the microbiota, and its interactions with the host. Additionally, there are other host factors that contribute to disease and gut microbiota composition, such as age, BMI and medication, as well as host metabolism and immune response. This makes it very difficult to distinguish cause from effect in correlation-based studies.
In short: it is all much more complicated than you think and separating the cause and effect is something no-one has managed to do convincingly yet. It's possible that the microbiome health really is as important as some people think, but it's also possible that the role is more minor and the changes in it associated with various diseases is just incidental.