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

•Interactions between animal hosts and their microbiota occur at multiple scales.•The zebrafish is a powerful model to study many scales of host-microbe interactions.•Gnotobiotic experiments provide fine scale resolution to identify molecular interactions.•Live imaging reveals dynamics of host-microbe interactions with cellular resolution.•Population level studies explore the host and microbe traits that shape microbiota.

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.

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