Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish
Michelle S. Massaquoi,
Garth L. Kong,
Daisy Chilin-Fuentes,
Julia S. Ngo,
Patrick F. Horve,
Ellie Melancon,
M. Kristina Hamilton,
Judith S. Eisen,
Karen Guillemin
Affiliations
Michelle S. Massaquoi
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA; Thermo Fisher Scientific, 22025 20th Avenue SE, Bothell, WA 98021, USA
Garth L. Kong
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
Daisy Chilin-Fuentes
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
Julia S. Ngo
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
Patrick F. Horve
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
Ellie Melancon
Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
M. Kristina Hamilton
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA
Judith S. Eisen
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
Karen Guillemin
Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Humans and the Microbiome Program, CIFAR, Toronto, ON M5G 1M1, Canada; Corresponding author
Summary: Animal development proceeds in the presence of intimate microbial associations, but the extent to which different host cells across the body respond to resident microbes remains to be fully explored. Using the vertebrate model organism, the larval zebrafish, we assessed transcriptional responses to the microbiota across the entire body at single-cell resolution. We find that cell types across the body, not limited to tissues at host-microbe interfaces, respond to the microbiota. Responses are cell-type-specific, but across many tissues the microbiota enhances cell proliferation, increases metabolism, and stimulates a diversity of cellular activities, revealing roles for the microbiota in promoting developmental plasticity. This work provides a resource for exploring transcriptional responses to the microbiota across all cell types of the vertebrate body and generating new hypotheses about the interactions between vertebrate hosts and their microbiota.
