Gene expression profile of Scardovia spp. in the metatranscriptome of root caries

Abstract A few investigations of caries biofilms have identified Scardovia spp.; however, little is known about its involvement in caries pathogenesis. The purpose of this study was to assess the gene expression profile of Scardovia spp. in root caries, and compare it with other microorganisms. Clinical samples from active root caries lesions were collected. Microbial mRNA was isolated and cDNA sequenced. The function and composition of the Scardovia were investigated using two methods: a) de novo assembly of the read data and mapping to contigs, and b) reads mapping to reference genomes. Pearson correlation was performed (p < 0.05). Proportion of Scardovia inopinata and Scardovia wiggsiae sequences ranged from 0-6% in the root caries metatranscriptome. There was a positive correlation between the transcriptome of Lactobacillus spp. and Scardovia spp. (r = 0.70; p = 0.03), as well as with other Bifidobacteriaceae (r = 0.91; p = 0.0006). Genes that code for fructose 6-phosphate phosphoketolase (the key enzyme for “Bifid shunt”), as well as ABC transporters and glycosyl-hydrolases were highly expressed. In conclusion, “Bifid shunt” and starch metabolism are involved in carbohydrate metabolism of S. inopinata and S. wiggsiae in root caries. There is a positive correlation between the metabolism abundance of Lactobacillus spp., Bifidobacteriaceae members, and Scardovia in root caries.

摘要 已有数项龋病生物膜相关研究检出斯卡多维亚菌属（Scardovia spp.），但目前对其在龋病致病机制中的作用仍知之甚少。本研究旨在分析根面龋中斯卡多维亚菌属的基因表达谱，并与其他微生物进行对比。研究收集了活动性根面龋损的临床样本，分离微生物mRNA并进行cDNA测序。通过两种方法探究斯卡多维亚菌属的功能与组成：a）对测序读长数据进行从头组装并比对至重叠群（contigs）；b）将读长比对至参考基因组。采用Pearson相关性分析（p < 0.05）。结果显示，根面龋宏转录组中，意外斯卡多维亚菌（Scardovia inopinata）与威格斯斯卡多维亚菌（Scardovia wiggsiae）的序列占比为0~6%。乳杆菌属（Lactobacillus spp.）与斯卡多维亚菌属的转录组呈正相关（r = 0.70; p = 0.03），同时与其他双歧杆菌科（Bifidobacteriaceae）成员也呈显著正相关（r = 0.91; p = 0.0006）。编码6-磷酸果糖磷酸酮醇酶（"双歧杆菌支路"关键酶）的基因、ABC转运蛋白（ABC transporters）以及糖苷水解酶（glycosyl-hydrolases）均呈高表达。综上，根面龋中意外斯卡多维亚菌与威格斯斯卡多维亚菌的碳水化合物代谢涉及"双歧杆菌支路"与淀粉代谢途径。根面龋中，乳杆菌属、双歧杆菌科成员与斯卡多维亚菌属的代谢丰度呈正相关。