Diversity analysis has been performed routinely on microbiomes, including human viromes. Shared species analysis has been conducted only rarely, but it can be a powerful supplement to diversity analysis. In the present study, we conducted integrated diversity and shared species analyses of human viromes by reanalyzing three published datasets of human viromes with more than 250 samples from healthy vs. diseased individuals and/or rural vs. urban individuals. We found significant differences in the virome diversity measured in the Hill numbers between the healthy and diseased individuals, with diseased individuals exhibiting higher virome diversity than healthy individuals, and rural individual exhibiting higher virome diversity than urban individuals. We applied both “read randomization” and “sample randomization” algorithms to perform shared species analysis. With the more conservative sample randomization algorithm, the observed number of shared species was significantly smaller than the expected shared species in 50% (8 of 16) of the comparisons. These results suggest that integrated diversity and shared species analysis can offer more comprehensive insights in comparing human virome samples than standard diversity analysis alone with potentially powerful applications in differentiating the effects of diseases or other meta-factors.

已经对微生物组（包括人类病毒组）进行了常规的多样性分析。共享物种分析很少进行，但它可以成为多样性分析的有力补充。在本研究中，我们进行了综合分集和共享物种通过重新分析人类viromes三个数据集出版与来自健康多于250个样本分析人类viromes的VS。患病个体和/或农村与. 城市个人。我们发现健康个体和患病个体之间以希尔数衡量的病毒组多样性存在显着差异，患病个体比健康个体表现出更高的病毒组多样性，农村个体比城市个体表现出更高的病毒组多样性。我们同时应用了“读取随机化”和“样本随机化”算法来执行共享物种分析。使用更保守的样本随机化算法，在 50%（16 个中的 8 个）比较中，观察到的共享物种数量明显小于预期共享物种。