The Hoops, Hopes, and Hypes of Human Microbiome Research

Abstract

Recent developments in sequencing methods and bioinformatics analysis tools have greatly enabled the culture-independent analysis of complex microbial communities associated with environmental samples, plants, and animals. This has led to a spectacular increase in the number of studies on both membership and functionalities of these hitherto invisible worlds, in particular those of the human microbiome. The wide variety in available microbiome tools and platforms can be overwhelming, and making sound conclusions from scientific research can be challenging. Here, I will review 1) the methodological and analytic hoops a good microbiome study has to jump through, including DNA extraction and choice of bioinformatics tools, 2) the hopes this field has generated for diseases such as autism and inflammatory bowel diseases, and 3) some of the hypes that it has created, e.g., by confusing correlation and causation, and the recent pseudoscientific commercialization of microbiome research.

Keywords: DNA extraction; microbial ecology; microbiome; microbiota; sequencing.

Figure 1

General overview of the workflow for 16S rRNA gene-based and metagenomic analysis of microbial communities, showing the most important steps and considerations for each stage of the process.