In rainbow trout, intestinal microbiota are known to influence a range of physiological functions, from proper epithelial development, to nutrient digestion, and immune activation. Microbiota colonize the trout gut at early life stages, even before exogenous feeding, and multiple studies have elucidated the role of environmental factors in regulating these early colonization dynamics. However, few studies have explored host-microbiota interaction during these early developmental stages, despite evidence that early colonization dynamics have a strong influence on the structure and function of microbiomes later in life. To study host-microbiota interactions in the gut of developing trout larvae, we characterized homeostatic intestinal transcription (RNAseq), and microbiota composition (16S rRNA gene sequencing) in two distinct lines of rainbow trout at early life-stages known to be critical in the development of host-microbe interactions (20- and 65-days post hatch). All female fish of both strains were reared in the same environment starting from eggs. Intestinal samples from 5 fish per group (2 trout strains x 2 developmental stages; 20 samples total) were used for mRNA-seq, while fifteen fish per group were sampled for gut microbiota analysis. RNAseq data was quantified at the transcript and gene level prior to testing for differential transcript usage and differential gene expression between the strains and developmental stages. Overall, 74 genes were shown to be differential transcribed (alternative splicing) (36.5% and 43.2% by strain and timepoint alone, respectively). At the gene level, 118 genes were differentially expressed between the two strains, while 2,413 genes were differentially expressed across timepoint (Fig. 1A). Gut microbiota followed a similar pattern to gene expression, with more differences observed by timepoint than by fish strain. Significant correlations in intestinal gene expression profiles and gut microbiota composition were also detected (Procrustes m2 = 0.19, Cor. = 0.90, p < 0.001), suggesting host and microbiota undergo ontogenetic development in concert. To further evaluate host regulation of gut microbes, gene co-expression networks were constructed, and gene modules were annotated (GO) and tested for correlation with the abundance of bacterial genera in the gut (Fig. 1B). These findings provide insights on host-microbe interactions at early stages by linking specific host gene co-expression modules to the abundance of specific bacterial genera.