Fig 2

(A) Schematic diagram of the protocol to evaluate the permanence of gnotobiotic larvae after 3 days of feeding, in which initially germ-free zebrafish is inoculated with three fluorescently labeled bacterial species. (B) Fraction of fluorescent colonies from plating whole larvae, indicating the fraction of intentionally inoculated bacteria, after 3 days of feeding and re-inoculation. (C) Total abundance of fluorescent bacteria per larva after 3 days of feeding and re-inoculation. (D) Abundance of each intentionally inoculated strain. PS: Pseudomonas mendocina ZWU0006, AE: Aeromona veronii ZOR0001, EN: Enterobacter cloacae ZOR0014. In panels B–D, each symbol indicates a measurement from an individual fish; boxes indicate the median and quartiles. (E) Maximum intensity projections of representative 3D image stacks from light sheet fluorescence microscopy of the guts of live larval fish, taken after 1 day of feeding with antibiotic- or UV-treated rotifers, or on the equivalent day for unfed fish. Each image is assembled from four or five scans of sub-regions that together span the whole gut, computationally registered after acquisition as described in Materials and Methods. Dashed lines trace approximate intestinal boundaries. Bar = 200 µm.