Dysbiosis and Its Discontents

Abstract

Dysbiosis is a key term in human microbiome research, especially when microbiome patterns are associated with disease states. Although some questions have been raised about how this term is applied, its use continues undiminished in the literature. We investigate the ways in which microbiome researchers discuss dysbiosis and then assess the impact of different concepts of dysbiosis on microbiome research. After an overview of the term's historical roots, we conduct quantitative and qualitative analyses of a large selection of contemporary dysbiosis statements. We categorize both short definitions and longer conceptual statements about dysbiosis. Further analysis allows us to identify the problematic implications of how dysbiosis is used, particularly with regard to causal hypotheses and normal-abnormal distinctions. We suggest that researchers should reflect carefully on the ways in which they discuss dysbiosis, in order for the field to continue to develop greater predictive scope and explanatory depth.

Keywords: dysbiosis; homeostasis; microbial diversity; microbiome; microbiota.

FIG 1

The contributions of Metchnikoff, Furney, and Scheunert to dysbiosis thinking. Metchnikoff photo from Les Prix Nobels 1908; Furney book cover from https://babel.hathitrust.org/cgi/pt?id=nnc1.1000947504;view=1up;seq=5; and Scheunert photo from http://www.ullmann-bernau.de/Ahnengemeinschaften (used with permission of the creator of the digital rendition, Steffen Ullmann [original photographer unknown]).

FIG 2

Helmut Haenel’s representations of dysbiosis and eubiosis. Image of Haenel used with permission of the Berlin-Brandenburgische Akademie der Wissenschaften. Figures of eubiosis and dysbiosis reconstructed from the work of Haenel (Fig. 4 and 5 in reference 16).

FIG 3

Definitions of dysbiosis. (A) Types of definitions with sample quotes, sometimes slightly paraphrased. References: , Maynard et al. (2012); , Arrieta et al. (2016); , Nibali et al. (2014); , Williams and Gallo (2015); , Lewis et al. (2015); , Youmans et al. (2015); , Lawley et al. (2012); , Jones et al. (2014); , Bested et al. (2013); , Sommer and Bäckhed (2013). (B) Popularity of different definitions.