The composition of the zebrafish intestinal microbial community varies across development

Abstract

The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another.

Figure 1

Experimental design and zebrafish development. (a) Experimental design showing important developmental events (top) and husbandry events (bottom) during the course of the study. The number of fish initially sampled among four tanks at each time point is shown, although post-sequencing rarefaction in some cases reduced this number for analyses (see Materials and Methods). Artemia are commonly called brine shrimp. Four and 10 d.p.f., fish are considered larvae, 21–35 d.p.f. fish are juveniles and 75 and 380 d.p.f. fish are adults. (b) The mean standard length and secreted IgM (sIgM) transcript levels (a proxy for adaptive immune development) of fish at sampled time points are shown with standard deviations. d.p.f., days post fertilization; ND, not determined.

Figure 2

Significant changes in diversity of individual zebrafish intestinal communities throughout development. (a) Number of observed taxa. (b) Faith's phylogenetic diversity. (c) Simpson's diversity index. Black circles and error bars represent the means and 95% confidence intervals, respectively. Letters above age groups indicate significant differences in the means.

Figure 3

Major shifts in bacterial taxa throughout development. Bacterial classes with >1% average relative abundance across all ages, plotted on a log scale (All taxonomic classes P<0.0001, Kruskal–Wallis).

Figure 4

Phylogenetic dissimilarity of microbiota from fish and environmental samples. (a) An non-metric multidimensional scaling (NMDS) ordination of (unweighted) UniFrac distances among zebrafish intestinal communities across development. Host age is differentiated by the color of points, while husbandry conditions (diet and water flow) are described in the legend. The age class of the host is indicated by the shape of points: circles indicate larvae, triangles indicate juveniles and squares indicate adults. The effect of standard length on the spread of points is shown by a vector. (b) Pairwise Unifrac distances among fish within each age group. (c) Pairwise Unifrac distances between fish and environmental communities at each age group. For each boxplot, letters above age groups indicate significant differences in the means.