… suggestions for optimizing experimental design and avoiding known pitfalls, organized in
the typical order in which studies are carried out. We first review best practices in experimental …

… Ideally, positive controls in microbiome research aid in correct data processing and the
parameters can be optimized with working positive controls. A frequently considered parameter is …

… the researchers’ results. Although I will primarily focus on examples from microbiome research,
… of microbiology, as all scientists struggle to ensure the reproducibility of their research. …

… Here we reviewed existing methodology studies and present suggestions for optimizing
research … in this exciting field to advance their studies while avoiding experimental artifacts. …

… pitfalls, analysis of the microbiome has not yet reached a maturity level enabling a consensus
in the scientific community regarding methods … , and optimizing methods and standards for …

… assays are optimized and validated … studies addressing the human microbiome have
undoubtedly been facilitated by advances in sequence-based methods, in some cases avoiding the …

… , and avoiding the computational expense of repeatedly re-analysing raw data using different
… To this end, awareness of pitfalls in performing and interpreting such analyses is required. …

… (A,B) Illustrate optimal crossover and parallel study design, highlighting that entry screening
… In this section, we outline the benefits and drawbacks of both options to help researchers …

… who incorporated microbiome analyses in their studies [… exposure can be mitigated by
avoiding the external layers and … extraction methods can degrade an originally optimal sample (…

… analysis strategies and pick the “optimal result” for each task. … “best” method in this way, by
validating the optimized results on … the necessity of avoiding questionable research practices. …