Replication of the published study entilted "Environmental factors shaping the gut microbiome in a Dutch population" - Gut microbiota and environmental characteristics in shaping disease occurrence

The composition and function of the gut microbiome are related to many human diseases. Many studies have shown that the intestinal microbiota and its metabolites are involved in the maintenance of intestinal homeostasis and intestinal immunity. Therefore, it is particularly important to determine the general characteristics of the microbiota in healthy or unhealthy people.
A recent study by Gacesa et al. based on the Lifelines dataset reported that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. The authors observed consistent microbiome-disease patterns across the majority of diseases, enabling them to pinpoint microbiome signatures that were shared between unrelated diseases as well as features that define a healthy microbiome. Specifically, 22 species selected by the statistical model were associated with more than 5 diseases, despite the low disease comorbidities in the cohort. 

We want to explore what is the determining factor (gut microbiota or environmental characteristics) for shaping disease differentiation. From Gacesa’s study, it seems that gut microbiota composition is an important factor in differentiating disease and healthy subjects. However, the major factor in shaping the occurrence of specific diseases, such as asthma, COPD and atopic dermatitis, is largely unclear.