Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America.
Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America.
PLoS One. 2019 Jan 30;14(1):e0199274. doi: 10.1371/journal.pone.0199274. eCollection 2019.
Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction.
Differences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins.
5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved-with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Data are available via ProteomeXchange with identifier PXD008845.
Metaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.
抗性淀粉是一种被肠道细菌代谢的益生元。它已被证明可减轻大鼠慢性肾脏病（CKD）的进展。以前的研究采用 16S rRNA 测序和非靶向代谢组学分析进行分类分析。在这里，我们通过宏蛋白质组学扩展了这些研究，从而深入了解宿主-微生物组的相互作用。
通过比较宏蛋白质组学分析，研究了给予含有抗性淀粉的饮食和给予可消化淀粉的饮食的 CKD 大鼠盲肠内容物之间的差异。使用独特的蛋白质序列获得分类学信息。我们的方法产生了涵盖宿主和细菌蛋白质的定量数据。
定量了 5834 种蛋白质，其中 947 种蛋白质来自宿主生物。从宏蛋白质组学数据中获得的分类学信息超过了以前的 16S RNA 分析，并且达到了中等丰度分类群的物种分辨率。特别是，瘤胃球菌科得到了很好的解析 - 丁酸产生菌和淀粉分解菌，如 R. bromii 清晰可见，明显升高，而纤维分解菌，如 R. flavefaciens 则明显降低，而用抗性淀粉喂养。蛋白质图谱的变化与纤维相关的 CKD 表型改善一致。几种已知的宿主 CKD 相关蛋白和肾功能受损的生物标志物在用抗性淀粉补充后显著降低。数据可通过 ProteomeXchange 以标识符 PXD008845 获得。
对有和没有抗性淀粉补充的 CKD 大鼠盲肠内容物进行宏蛋白质组学分析，以空前的分辨率揭示了肠道微生物群内的变化，提供了功能和分类学信息。用 RS 补充时丰度不同的蛋白质和生物体表明，从粘蛋白降解菌向丁酸产生菌转变。
