Issues and current standards of controls in microbiome research

Bastian V H Hornung; Romy D Zwittink; Ed J Kuijper

doi:10.1093/femsec/fiz045

Issues and current standards of controls in microbiome research

FEMS Microbiol Ecol. 2019 May 1;95(5):fiz045. doi: 10.1093/femsec/fiz045.

Authors

Bastian V H Hornung^{1

2}, Romy D Zwittink^{1

2}, Ed J Kuijper^{1

2

3}

Affiliations

¹ Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.
² Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.
³ Netherlands Donor Feces Bank, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.

Abstract

Good 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.

Keywords: best practices; contamination; metagenomics; microbiome; microbiota; negative control; positive control.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Humans
Microbiota*
Reproducibility of Results
Research / standards*