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Integrated diversity and shared species analyses of human viromes

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Abstract

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.

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Acknowledgements

This research received funding from the following sources: NSFC (Grant No. 31970116) to MA, “The Yunnan provincial department of education scientific research fund project” (No. 2019J0646) to HJC, #GREKF19-07 to HJC, and #GREKF20-06 to QL, both from “State Key Laboratory of Genetic Resources and Evolution”

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Authors and Affiliations

  1. Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China

    Yuting Qiao, Shutao Li, Hongju Chen & Zhanshan (Sam) Ma

  2. Physiatrics Medicine, Yan’an Hospital of Kunming City, Kunming, China

    Jianmei Zhang

  3. College of Mathematics, Honghe University, Mengzi, Yunnan, China

    Qiang Liu & Hongju Chen

  4. Physical Examination Center, Affiliated Hospital of Yunnan University, Kunming, China

    Qiang Wang

  5. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China

    Zhanshan (Sam) Ma

Authors
  1. Yuting Qiao
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  2. Shutao Li
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  3. Jianmei Zhang
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  4. Qiang Liu
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  5. Qiang Wang
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  6. Hongju Chen
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  7. Zhanshan (Sam) Ma
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Contributions

YTQ wrote the manuscript and interpret the results. STL prepared the figures. JMZ, QW and QL participated in interpretations of results. YTQ and HJC performed data analysis. ZSM designed the study. All authors approved the submission.

Corresponding author

Correspondence to Zhanshan (Sam) Ma.

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Qiao, Y., Li, S., Zhang, J. et al. Integrated diversity and shared species analyses of human viromes. Arch Virol 166, 2743–2749 (2021). https://doi.org/10.1007/s00705-021-05157-0

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  • DOI: https://doi.org/10.1007/s00705-021-05157-0

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