Koo Hyunmin, Hakim Joseph A, Powell Mickie L, Kumar Ranjit, Eipers Peter G, Morrow Casey D, Crowley Michael, Lefkowitz Elliot J, Watts Stephen A, Bej Asim K
Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
Biomedical Informatics, Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL, USA.
J Microbiol Methods. 2017 Apr;135:69-76. doi: 10.1016/j.mimet.2017.01.016. Epub 2017 Feb 3.
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using a metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine. The CFD-fed D. rerio exhibited KEGG functional categories of bacteria-mediated cobalamin biosynthesis, which was supported by the presence of cobalamin synthesizers such as Bacteroides and Lactobacillus. Though these bacteria were absent in GFD-fed D. rerio, a comparable level of the cobalamin biosynthesis KEGG functional category was observed, which could be contributed by the compensatory enrichment of Cetobacterium. Based on these results, we conclude D. rerio to be a suitable alternative animal model for the use of a targeted metagenomics approach along with bioinformatics tools to further investigate the relationship between the gluten diet and microbiome profile in the gut ecosystem leading to gastrointestinal diseases and other undesired adverse health effects.
在本研究中，我们使用宏基因组学方法和生物信息学工具，报告了喂食对照配方饲料（CFD）和麸质配方饲料（GFD）的斑马鱼（Danio rerio）的肠道微生物组成及预测功能概况。与喂食CFD的斑马鱼相比，喂食GFD的斑马鱼的微生物群落中军团菌目、根瘤菌科和红杆菌的丰度更高。喂食GFD的斑马鱼的微生物群落的预测宏基因组学（PICRUSt）显示出与胆汁分泌、次级胆汁酸生物合成以及甘氨酸、丝氨酸和苏氨酸代谢相对应的KEGG功能类别。喂食CFD的斑马鱼表现出细菌介导的钴胺素生物合成的KEGG功能类别，这得到了诸如拟杆菌属和乳杆菌属等钴胺素合成菌的存在的支持。虽然在喂食GFD的斑马鱼中不存在这些细菌，但观察到了相当水平的钴胺素生物合成KEGG功能类别，这可能是由鲸杆菌的代偿性富集所致。基于这些结果，我们得出结论，斑马鱼是一种合适的替代动物模型，可用于采用靶向宏基因组学方法和生物信息学工具，进一步研究麸质饮食与肠道生态系统中微生物组概况之间的关系，这种关系会导致胃肠道疾病和其他不良健康影响。
