Quantitative assessment of NCLDV-host interactions predicted by co-occurrence analyses [article]

Lingjie Meng, Hisashi Endo, Romain Blanc-Mathieu, Rodrigo Hernandez-Velazquez, Hiroto Kaneko, Hiroyuki Ogata
2020 bioRxiv   pre-print
Nucleocytoplasmic DNA viruses (NCLDVs) are highly diverse and abundant in marine environments. However, knowledge of their hosts is limited because only a few NCLDVs have been isolated. By taking advantage of the rapidly increasing metagenomic data, in silico host prediction approaches are expected to fill this gap between known virus-host relationships and the true but largely unknown amount of NCLDVs. In this study, we built co-occurrence networks between NCLDVs and eukaryotes using the Tara
more » ... ceans metagenome and metabarcoding datasets to predict virus-host interactions. Using the positive likelihood ratio to assess the performance of host prediction for NCLDVs, we demonstrated that co-occurrence approaches can increase the odds of predicting true positive relationships four-fold compared with random host predictions in the high-weight region (weight > 0.4). To refine the host predictions from high-dimensional co-occurrence networks, we employed a recently proposed phylogeny-based method, Taxon Interaction Mapper, and showed that Taxon Interaction Mapper further improved the prediction performance eight-fold using weight cut-off filtration (> 0.4). Finally, we inferred virophage and NCLDV networks that further corroborated that co-occurrence approaches are effective for predicting NCLDV hosts in marine environments.
doi:10.1101/2020.10.16.342030 fatcat:a3am2xfworfobo5kbzxiqigl2m