1Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.
2Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA.
J Gen Virol. 2018 Aug;99(8):1141-1146. doi: 10.1099/jgv.0.001097. Epub 2018 Jun 11.
Viruses are the most abundant component of the human microbiota. Recent evidence has uncovered a rich diversity of viruses within the female bladder, including both bacteriophages and eukaryotic viruses. We conducted whole-genome sequencing of the bladder microbiome of 30 women: 10 asymptomatic 'healthy' women and 20 women with an overactive bladder. These metagenomes include sequences representative of human, bacterial and viral DNA. This analysis, however, focused specifically on viral sequences. Using the bioinformatic tool virMine, we discovered sequence fragments, as well as complete genomes, of bacteriophages and the eukaryotic virus JC polyomavirus. The method employed here is a critical proof of concept: the genomes of viral populations within the low-biomass bladder microbiota can be reconstructed through whole-genome sequencing of the entire microbial community.
病毒是人类微生物群中最丰富的组成部分。最近的证据揭示了女性膀胱中存在丰富多样的病毒，包括噬菌体和真核病毒。我们对 30 名女性的膀胱微生物组进行了全基因组测序：10 名无症状“健康”女性和 20 名膀胱过度活动症女性。这些宏基因组包括代表人类、细菌和病毒 DNA 的序列。然而，这项分析专门针对病毒序列。使用生物信息学工具 virMine，我们发现了噬菌体和真核病毒 JC 多瘤病毒的序列片段以及完整基因组。这里采用的方法是一个关键的概念验证：通过对整个微生物群落进行全基因组测序，可以重建低生物量膀胱微生物群中病毒群体的基因组。
