Conclusions
We are currently at a major turning point on how we can derive valuable insights on the ecological processes shaping non-model and environmental microbiomes in the wild. The adoption of robust laboratory and bioinformatic techniques, together with sophisticated statistical approaches, enhance our ability to gain deeper insights into the factors influencing microbiome variation and the intricate relationships among microbial taxa. However, all of these techniques rely on robust study designs and appropriate sampling scales to address specific research questions. Ultimately, this perspective piece serves as a broad outline of some of the considerations that ought to be considered in the field of microbiome ecology. Hopefully, with robust practices, we can, in turn, start to untangle the complex processes acting on these incredibly important but understudied communities.