RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro.
RNA-Based Stable Isotope Probing Suggests Allobaculum spp. as Particularly Active Glucose Assimilators in a Complex Murine Microbiota Cultured In Vitro.
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DOI：
10.1155/2017/1829685
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发表时间：
2017
影响因子：
--
通讯作者：
Egert M
中科院分区：
文献类型：
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作者：
Herrmann E;Young W;Rosendale D;Reichert-Grimm V;Riedel CU;Conrad R;Egert M
基于RNA的稳定同位素探测（RNA-SIP）和代谢分析用于检测从小鼠模型系统获得的复杂微生物群落中的活跃葡萄糖消耗细菌。将粪便来源的微生物群在厌氧条件下用40 mM [U13C]葡萄糖孵育0、2和4 h。等密度密度梯度超离心分离和分馏分离的RNA标记和未标记的馏分，然后通过16S rRNA测序显示了一个快速适应的细菌群落响应于添加的糖，这是占主导地位的未分类毛螺菌科物种。同位素标记的RNA的不同部分的检查显示Allobaculum spp.作为系统中特别活跃的葡萄糖利用者，因为相应的RNA在标记的RNA中显示出显著更高的比例。随着时间的推移，标记的糖被更广泛的粪便细菌使用。代谢分析表明[U13 C]葡萄糖的快速发酵，乳酸盐，乙酸盐和丙酸盐是主要的13 C标记的发酵产物，并建议在系统中发生“交叉喂养”。RNA-SIP结合13C标记产物的代谢谱分析允许深入了解一般模型底物的微生物同化，证明了该技术在作为模型系统的小鼠肠道微生物群中研究营养上更相关的底物（例如益生元碳水化合物）的同化过程的适当性。
RNA-based stable isotope probing (RNA-SIP) and metabolic profiling were used to detect actively glucose-consuming bacteria in a complex microbial community obtained from a murine model system. A faeces-derived microbiota was incubated under anaerobic conditions for 0, 2, and 4 h with 40 mM [U13C]glucose. Isopycnic density gradient ultracentrifugation and fractionation of isolated RNA into labeled and unlabeled fractions followed by 16S rRNA sequencing showed a quick adaptation of the bacterial community in response to the added sugar, which was dominated by unclassified Lachnospiraceae species. Inspection of distinct fractions of isotope-labeled RNA revealed Allobaculum spp. as particularly active glucose utilizers in the system, as the corresponding RNA showed significantly higher proportions among the labeled RNA. With time, the labeled sugar was used by a wider spectrum of faecal bacteria. Metabolic profiling indicated rapid fermentation of [U13C]glucose, with lactate, acetate, and propionate being the principal 13C-labeled fermentation products, and suggested that “cross-feeding” occurred in the system. RNA-SIP combined with metabolic profiling of 13C-labeled products allowed insights into the microbial assimilation of a general model substrate, demonstrating the appropriateness of this technology to study assimilation processes of nutritionally more relevant substrates, for example, prebiotic carbohydrates, in the gut microbiota of mice as a model system.