The scales of the zebrafish: host-microbiota interactions from proteins to populations

The interactions between animal hosts and their associated microbiota can be studied at multiple spatial and conceptual scales, with each providing unique perspectives on the processes structuring host-microbe systems. Recently, zebrafish, Danio rerio, has emerged as a powerful model in which to study these interactions at many different scales. Controlled but simplified gnotobiotic experiments enable discovery of the molecules and cellular dynamics that shape host-microbe system development, whereas population level investigations of bacterial dispersal and transmission are beginning to reveal the processes shaping microbiota assembly across hosts. Here we review recent examples of these studies and discuss how the results can be integrated to better understand host-microbiota systems.