Equally contributing first authors in bold

Conflict of interest statement

P.C.K.: Advisory Board of Novome Biotechnologies, ad hoc consultant for Pendulum Therapeutics, IP group inc., and Otsuka Pharmaceuticals.

D.B.K.: D.B.K. serves as CEO of CoreBiome, a company involved in the commercialization of microbiome analysis and a wholly owned subsidiary of OraSure Technologies. These interests have been reviewed and managed by the University of Minnesota in accordance with its Conflict-of-Interest policies.

Author contributions to manuscript

D.K, S.A.H, and P.C.K. designed the experiments and the overall data analysis. K.A.M, R.A.T.M., A.J.J., and P.C.K. wrote the manuscript with input from co-authors. H.R.L. and P.C.K. coordinated human subject recruiting and sampling. T.W., H.R.L., L.D contributed to sample processing data generation and analysis. K.A.M, R.A.T.M., A.J.J., and T.Z. analyzed data. S.P., A.J.J., and R.A.T.M. performed data integration. K.R.K, R.B., M.D., G.F., D.K., S.A.H, and P.C.K directed research and provided critical feedback. G.F. and P.C.K. performed clinical data analysis.

Materials availability statement

Supplementary dataset with viral contig counts and Supplementary tables can be accessed on Mendeley Data http://dx.doi.org/10.17632/rvcv3t326p.4

All other data, analytic methods, and study materials will be made available to other researchers when possible.

Acknowledgments

The authors like to thank Lyndsay Busby for secretarial assistance, and Rosemary Mihindukulasuriya for help with creating figures. This work was supported by NIH grant DK114007 (P.C.K.), the Center for Individualized Medicine, Mayo Clinic, Rochester, MN (P.C.K.); the Minnesota Partnership for Biotechnology and Medical Genomics (P.C.K. and D.K.); and NIH grant 5RC2DK116713-02 (S.A.H.).

The gut virome is temporally stable, can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.