文章：Metagenomic Pyrosequencing and Microbial Identification

杂志：Clin Chem

年份：2009

80% of bacteria identified by metagenomic sequencing were considered noncultivable.（80%的菌是不能体外培养的）

Pathogen identification in infectious diseases relies mostly on routine cultures and biochemical testing using semi-automated platforms in the clinical laboratory.（病毒的检测是利用培养和生化检测、半自动化的视线）

数据库：The oldest and most traditional bacterial classification system is based on Bergey’s taxonomy which has attempted to merge phenotypic (e.g. biochemical) and molecular data to create a higher-order taxonomy in recent years. More recently developed taxonomic schemes include systems proposed by Pace, Ludwig, Hugenholtz, and the NCBI. Multiple on-line databases have been developed on the basis of these different taxonomic schemes and provide convenient access to large ribosomal RNA sequence databases for clinical laboratories and research teams. The most prominent databases include the Ribosomal Database Project II (RDP II) (http://rdp.cme.msu.edu/), Greengenes (greengenes.lbl.gov), and ARB-Silva.

   RDP II is based on Bergey’s taxonomy which contains a relatively small number of phyla.

   Greengenes includes multiple taxonomic schemes so that query results with this database can be compared using different classification systems.

   The ARB-Silva database also offers a choice of microbial taxonomies, although it is more limited in its flexibility than Greengenes.

   不同的数据库之间有较大区别，这个需要注意，那反过来讲，针对各自的科研目的，选择什么样的数据库是最合适的？不同的数据库具体区别在哪？对研究结果的具体影响是什么？

   As a case in point, the Pace and Hugenholtz lineages separately named 12 phylum-level lineages, and RDP II had not named any of these lineages. The taxonomic schemes varied with respect to numbers of phyla, for example, with a maximum of 88 phyla for the Pace and Hugenholtz curations and 31 phyla for the RDP (based on Bergey’s) classification system.