Abstract
ABSTRACTGood scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the ‘scientific reproducibility crisis’. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.
Highlights
The microbiome field is a relatively new field of research
While the field of microbiome studies has become an established research area, and many best practices exist (Goodrich et al 2014; Boers, Jansen and Hays 2016; Kim et al 2017; Knight et al 2018; Martin et al 2018; Pollock et al 2018), they have not gone in-depth regarding the usage of controls
We summarized the issues regarding good scientific practice in light of controls, to make scientists aware of these issues, so that they can be addressed in their own research
Summary
The microbiome field is a relatively new field of research. The hallmark publication by (Venter et al 2004) is not even 15 years old. If this is the case for some species in the positive control, the researcher will get assignments on e.g. the respective family level, and will be made aware of this restriction and can interpret his data with this in mind.
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