Drivers of Variation of the Zebrafish Egg Microbiome

Microbiomes are integral to the fitness of many animals, yet little is known about early-life microbiome assembly. What is known largely comes from studies in non-model organisms, where it is difficult to distinguish host genetics from the environment as drivers of microbiome assembly. Here, we used a popular vertebrate model, zebrafish (Danio rerio), to address the major drivers of environmental assembly in 124 individuals. We surveyed the egg microbiome from fertilization to hatching using 16S rRNA gene sequencing and investigated development stage and parentage as potential drivers of microbiome variation. Phylogenetic diversity of the egg microbiome decreased during development, suggesting that environmental filtering may be a major driver of community assembly. Parentage also had an influence on microbiome assembly; eggs derived from the same clutch were often more similar in microbiome composition compared to eggs derived from different clutches. The effect of parentage on microbiome similarity decreased over development, suggesting that parents may be an initial source of egg microbiome members. The egg microbiome undergoes dramatic compositional shifts during development. Understanding the drivers of this variation is important to consider, especially given the role of the microbiome in health and development, and that early exposure to microbes may shape later animal development. Our findings suggest that parents may serve as an important source of microbial symbionts to their offspring, even in an animal that does not provide parental care, such as laboratory zebrafish, and that the developing egg may play an increasingly important role in driving microbiome variation across individuals. ImportanceEarly-life microbiome composition is integral for establishing the normal functioning of multiple host systems, including the nervous system, gastro-intestinal tract, and immune system. However, the drivers of variation in early-life microbiome composition are underexplored, especially in Danio rerio (zebrafish), an important model organism that has allowed extensive exploration of the role of the microbiome in host health and development. Here, we characterize the microbiome of individual zebrafish eggs and determine the effects of parental identity and developmental time on shaping the egg microbiome prior to hatching. Both parentage and age influence microbiome composition and diversity. We found evidence that species-sorting (i.e. selection of microbes by the egg) is an important driver of microbiome assembly during egg development. Furthermore, the effect of parentage on the microbiome, while significant throughout embryonic development, decays over time. Despite the lack of parental care in laboratory reared zebrafish, these findings suggest that the parents are significant source of microbes to their offspring.