Wanyama Jeremiah W, Okyere Lydia, Duan Luoyan, Gaulke Christopher A
Department of Pathobiology, University of Illinois Urbana Champaign.
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign.
bioRxiv. 2025 May 8:2025.05.08.652836. doi: 10.1101/2025.05.08.652836.
The zebrafish () 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.
斑马鱼已成为研究宿主与微生物组相互作用的重要动物模型。然而，关于实验参数的变化如何影响成年斑马鱼微生物组的结构和功能的信息有限，这使得实验设计、结果解读变得复杂，并可能降低可重复性。在这里，我们使用16S rRNA扩增子测序量化了微生物组变异的两个潜在来源——饲养策略和采样位置——对成年斑马鱼微生物多样性的影响。我们的研究结果表明，饲养策略显著影响成年鱼的肠道微生物组多样性，在循环水系统中共饲养的个体之间相似度最高。饲养转移后微生物组的适应需要14至21天。在不同采样点也观察到微生物组组成的显著差异。与人类一样，粪便和肠道微生物群落相似且因性别而异，然而每个采样的身体部位都有一个小的部位特异性微生物群落特征。同样，这些群落的推断功能表明，基因家族多样性预计也会因身体部位而异，尤其是在肠道和非肠道部位之间。我们的工作共同表明，饲养、性别和采样策略都会显著影响微生物群落组成，并强调需要就成年斑马鱼微生物组研究的最佳实践和报告标准进行全领域的讨论。
