Influence of Housing, Sex, and Sampling Location on Taxonomy and Function of Adult Zebrafish Microbiomes

The zebrafish (Danio rerio) has emerged as an important animal model for the study of host-microbiome interactions. However, information on how variation in experimental parameters contribute to microbiome structure and function in adult zebrafish is limited which complicates experimental design, interpretation of results, and may reduce reproducibility. Here we quantified the impact of two potential sources of microbiome variation - housing strategy and sampling location - on microbial diversity of adult zebrafish using 16S rRNA amplicon sequencing. Our findings indicate that housing strategy significantly impacts gut microbiome diversity in adult fish with the highest similarity between individuals co-housed on recirculating water systems. Microbiome acclimation after housing transfer took between 14- and 21-days. Significant variation in microbiome composition was also observed across sampling sites. As in humans, fecal and intestinal microbial communities were similar and varied by sex, however each body site sampled possessed a small site-specific microbial community signature. Consistently, imputed function of these communities showed that gene family diversity is also predicted to vary by body site particularly between gut and non-gut locations. Together our work demonstrates that housing, sex, and sampling strategy all significantly impact microbial community composition and highlight the need for community wide discussions on best practices and reporting standards for adult zebrafish microbiome studies.