Wommack K Eric, Bench Shellie R, Bhavsar Jaysheel, Mead David, Hanson Tom
Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Methods Mol Biol. 2009;502:279-89. doi: 10.1007/978-1-60327-565-1_16.
Current appreciation of the vast expanse of prokaryotic diversity has largely come through molecular phylogenetic exploration of sequence diversity within the universally conserved gene for small subunit ribosomal RNA (16S rDNA). A plethora of methodologies for characterizing the diversity and composition of bacterial communities is based on sequence polymorphisms within this single gene. By comparison, no gene is universally shared among viruses or bacteriophages, which has prevented broad scale characterization of viral diversity within microbial ecosystems. With the reduction in DNA sequencing costs and wide availability of bioinformatics software, the tools of whole genome shotgun sequencing are now beginning to be applied to the characterization of genetic diversity within whole microbial communities. Such metagenomic approaches are ideally suited to the characterization of natural assemblages of viruses, because of the typically small, coding-dense nature of viral genomes. Data from a limited number of characterized viral metagenome libraries within a range of microbial ecosystems indicates that viral assemblages are comprised of between approximately 1,000 to a million different genotypes. Furthermore, viral assemblages typically contain a large proportion of completely novel genes and are likely to be the largest reservoir of unexplored genetic diversity on earth. Here, we present a conceptual framework for characterization of viral assemblages through metagenomic approaches.
目前对原核生物多样性广泛程度的认识，很大程度上来自于对小亚基核糖体RNA（16S rDNA）普遍保守基因内序列多样性的分子系统发育探索。大量用于表征细菌群落多样性和组成的方法都是基于这个单一基因内的序列多态性。相比之下，病毒或噬菌体之间没有普遍共享的基因，这阻碍了对微生物生态系统内病毒多样性的大规模表征。随着DNA测序成本的降低和生物信息学软件的广泛应用，全基因组鸟枪法测序工具现在开始应用于整个微生物群落内遗传多样性的表征。由于病毒基因组通常具有小而编码密集的特点，这种宏基因组学方法非常适合表征病毒的自然组合。来自一系列微生物生态系统中有限数量的已表征病毒宏基因组文库的数据表明，病毒组合由大约1000到100万个不同的基因型组成。此外，病毒组合通常包含很大比例的全新基因，并且可能是地球上未探索遗传多样性的最大储存库。在这里，我们提出了一个通过宏基因组学方法表征病毒组合的概念框架。
