Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta’s optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.
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Accession numbers of all publicly available metagenomes used for analysis are provided in Supplementary Table 11. Source data for individual figures are provided with this manuscript. Phanta’s databases are available from the links specified at https://github.com/bhattlab/phanta (ref. 45). There are no restrictions on data availability. Source data are provided with this paper.
Workflows were used for the preprocessing and assembly steps described in Methods and the workflows are available at https://github.com/bhattlab/bhattlab_workflows. Phanta and its postprocessing scripts are publicly available at https://github.com/bhattlab/phanta (ref. 45) with a detailed tutorial describing installation and usage.
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We thank D. Maghini and B. Doyle for thoughtful comments on the manuscript; S. Nayfach, P. Hiseni, S. Salzberg and J. Lu for helpful conversations; B. Doyle and J. Wirbel for testing Phanta; and B. Siranosian, C. Nicolau, K. Bettinger, A. Behr and the Stanford Research Computing Center for computational support. Computing costs were supported, in part, by an NIH S10 Shared Instrumentation under grant 1S10OD02014101. Figure 1 was created using BioRender.com. This study was supported in part by NIH R01AI148623 and R01AI143757, a Stand Up 2 Cancer Grant, the Chan Zuckerberg Initiative, a Sloan Foundation Fellowship and the Allen Distinguished Investigator Award (to A.S.B.). Y.P. is supported by the School of Medicine Dean’s Postdoctoral Fellowship. M.C. was supported by an NIH-funded predoctoral fellowship (5T32HG000044-25) and is supported by the National Defense Science and Engineering Graduate Fellowship (starting September 2022).
The authors declare no competing interests.
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Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut microbiomes with Phanta. Nat Biotechnol (2023). https://doi.org/10.1038/s41587-023-01799-4