Whole metagenome shotgun sequencing is a powerful approach to detect the functional potential of microbial communities. Currently, the read-based metagenomics profiling for established database (RBED) method is one of the two kinds of conventional methods for species and functional annotations. However, the databases, which are established based on test samples or specific reference genomes or protein sequences, limit the coverage of global microbial diversity. The other assembly-based metagenomics profiling for unestablished database (ABUD) method has a low utilization rate of reads, resulting in a lot of biological information loss. In this study, we proposed a new method, read-based metagenomics profiling for unestablished database (RBUD), based on Metagenome Database of Global Microorganisms (MDGM), to solve the above problems. To evaluate the accuracy and effectiveness of our method, the intestinal bacterial composition and function analyses were performed in both avian colibacillosis chicken cases and type 2 diabetes mellitus patients. Comparing to the existing methods, RBUD is superior in detecting proteins, percentage of reads mapping and ontological similarity of intestinal microbes. The results of RBUD are in better agreement with the classical functional studies on these two diseases. RBUD also has the advantages of fast analysis speed and is not limited by the sample size.

中文翻译：

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RBUD：一种用于全微生物基因组鸟枪法测序的新功能潜力分析方法

全宏基因组鸟枪法测序是检测微生物群落功能潜力的有效方法。目前，基于读取的宏基因组分析建立数据库（RBED）方法是物种和功能注释的两种常规方法之一。然而，基于测试样本或特定参考基因组或蛋白质序列建立的数据库限制了全球微生物多样性的覆盖范围。另一种基于组装的未建立数据库宏基因组分析（ABUD）方法的读取利用率较低，导致大量生物信息丢失。在本研究中，我们提出了一种基于全球微生物宏基因组数据库（MDGM）的新方法，即基于读取的未建立数据库宏基因组分析（RBUD），以解决上述问题。为了评估我们方法的准确性和有效性，对禽大肠杆菌病鸡病例和2型糖尿病患者进行了肠道细菌组成和功能分析。与现有方法相比，RBUD 在检测蛋白质、读数映射百分比和肠道微生物本体相似性方面具有优越性。RBUD 的结果与这两种疾病的经典功能研究更加一致。RBUD还具有分析速度快、不受样本量限制等优点。