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Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Abstract

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.

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Data availability

Sequence data that support the findings of this study have been deposited in GenBank under BioProject accession PRJNA510571 and at https://github.com/linsalrob/crAssphage. Each of the samples has a unique BioSample accession number (SAMN10656826SAMN10658627, SAMN10658653 and SAMN10659294). The SRA runs used in this analysis are included in Supplementary File 5. The data that support the findings of this study are also available from the corresponding authors on reasonable request.

Code availability

The code used to generate the data can be accessed at https://github.com/linsalrob/crAssphage. The current release81 is v.2.0.

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Acknowledgements

We thank R. Matthews, M. Wright, J. Alexander, S. Arredondo, N. Branch, D. Campbell, R. Chea, D. McDougle, J. Parks and V. Vipatapat for providing access to wastewater treatment samples; the members of the Mountain Gorilla Veterinary Project and the staff of Maryland Zoo for collecting the gorilla faecal samples in Rwanda; G. Britton for collecting the baboon faecal samples in Ethiopia; staff of the CSWCT, the UWA and the UNCST for collecting the chimpanzee faecal samples in Uganda; J. Manor at Central Virology Laboratory, Chaim Sheba Medical Center, Tel-Hashomer Hospital and G. Steward, Department of Oceanography, University of Hawai’i at Manoa for help with sample collection; the COMPARE and LifeLines-DEEP projects for sharing data; O.D.N. thanks G. Steward, University of Hawai’i, Manoa for support. P.C.F. thanks C. Taylor for support with the PCR. Primate samples were provided by the PMC at the University of Illinois Urbana-Champaign; D.T.M. thanks the Australian Research Council’s Linkage Project LP160100408, Melbourne Water and EPA Victoria for funding the collection of samples in Melbourne. Gorilla samples were originally obtained by M.K. and the Mountain Gorilla Veterinary Project in Rwanda. G.R. and N.J.D. provided the wild baboon samples from Ethiopia. Howler samples were provided by M.K. and lemur samples were provided by R.E.J. and M.T.I., R.M.S. and L.M. provided the chimpanzee samples with permission from the CSWCT, the UWA and the UNCST. The primate microbiome project was supported by NSF BCS 0935347 to S.L., R. Stumpf, B.W. and K. Nelson. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This work used the XSEDE Jetstream resources at Indiana University and Texas Advanced Computing Center through allocation MCB170036 to R.A.E., which is supported by National Science Foundation grant number ACI-1548562. Some of this work was supported by San Diego State University Grants Programs to R.A.E., including the Summer Undergraduate Research Program. This work was supported by National Science Foundation grant numbers MCB-1441985 to R.A.E. and DUE-1323809 to E.A.D; the Department of Energy Lawrence Livermore National Laboratory grant B618146 to R.A.E., P.A.d.J. and B.E.D. were supported by the NWO Vidi grant 864.14.004; F.L.N. by the NWO Veni grant 016.Veni.181.092; S.J.J.B. by the European Research Council Stg grant (638707) and the Vidi grant 864.11.005; O.C. and K. Mazankova by the Ministry of Health of the Czech Republic grant numbers 15-31426A and 15-29078A; P.C.F. by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. J.J.B. by the ARC Discovery Early Career Researcher Award (DE170100525); S.L.D.M. by an NIH Pathway to Independence Fellowship (1K99AI119401-01A1); K.B. by award number 1510925 from the United States National Science Foundation; M.T.I. by National Geographic Society (CRE) and NSERC; and C.D. by the Agence Nationale de la Recherche JCJC grant ANR-13-JSV6-0004 and Investissements d’Avenir Méditerranée Infection 10-IAHU-03. The LifeLines-DEEP sample collection and analysis was funded by the Netherlands Heart Foundation (IN-CONTROL CVON grant 2012-03) to A.Z. and J.F., by the Top Institute Food and Nutrition, Wageningen, the Netherlands (TiFN GH001) to C.W., by NWO Vidi grants 864.13.013 to J.F. and 016.178.056 to A.Z., NWO Spinoza Prize SPI 92-266 to C.W., and by the ERC FP7/2007-2013/ERC Advanced Grant agreement 2012-322698 to C.W., ERC Starting Grant 715772 to A.Z. A.Z. also holds a Rosalind Franklin Fellowship from the University of Groningen. The COMPARE data collection was funded by The Novo Nordisk Foundation (NNF16OC0021856).

Author information

B.E.D. and R.A.E. conceived the study, performed the experiments and bioinformatics, and wrote the paper with input from all authors. A.A.V. performed the volunteer experiments and sampled San Diego wastewater treatment plants. F.L.N., H.M.N., M.O. and P.A.d.J. performed human volunteer experiments. A.M.E., A.R., A.T., D.A.C., J.M.H., K.L., K.McNair, T.C. and V.A.C. performed bioinformatics analysis. A.A.R.R., A.Alassaf, A.C., A.M., A.O., A.R.M., A.S.N., A.W., B.M.-G., B.M.E., C.D., C.F., C.H., D.C., D.K., D.T.M., E.A.D., E.B., E.N.I., E.N.S., E.S.L., G.A., G.C.-A., G.-S.C., G.T., H.H., H.N., J.A., J.J.B., J.J.T., J.M.C., J.M.M., J.W., K.B., K.L.W., K.Mazankova, L.C.S., L.D., M.A.U.I., M.K.M., M.L., M.M.Z., M.Morris, M.Muniesa, M.P., M.P.D., N.T., N.V., O.C., O.D.N., P.C., P.C.F., P.D., P.R., P.V., R.d.l.I., R.K.A., R.L., R.O., R.R., R.Santos, R.Strain, S.J.J.B., S.L.D.M., S.M., S.M.-M., S.W., T.C., T.J., U.Q. and Z.-X.Q. performed sampling, PCR and sequencing. A.K., A.Z., C.W. and J.F. performed the Lifelines analysis. F.M.A., H.Z. and R.S.H. provided and analysed COMPARE project data. A.Asangba, B.W., G.A.O.R., N.J.D., N.-p.N., R.Stumpf and S.L. analysed and provided the non-human primate sequences. M.C. collected gorilla samples. A.T., E.G. and K.M.G. performed the NYC sewage sampling and data analysis. A.J.P., J.S., L.C.M., P.J.T., S.R.H. and S.T.K. examined crAssphage transfer among infants. M.T.I. and R.E.J. collected lemur samples. M.K. collected howler monkey samples. D.L., K.R. created the map of the world figure. L.M. collected chimpanzee samples.

Correspondence to Robert A. Edwards or Bas E. Dutilh.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–9, Supplementary Tables 1–6 and Supplementary References.

Reporting Summary

Supplementary File 1

Global sampling of crAssphage: the metadata and sequence data for each of the amplicon regions.

Supplementary File 2

Gretel strains: number of strains identified from all of the different samples in the SRA.

Supplementary File 3

Lifelines phenotype correlations: correlation, P value and adjusted P value for 207 exogenous and intrinsic human variables, and the presence of crAssphage in stools.

Supplementary File 4

Lifelines microbial correlations: correlation, P value and adjusted P value for the presence of 491 bacterial isolates and the presence of crAssphage in stools.

Supplementary File 5

SRA Runs: the identities of all runs in the SRA with matches to crAssphage, including the number of sequences that match, the total bases aligned and the average coverage.

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Fig. 1: crAssphage presence or absence status over time in the human gut.
Fig. 2: Diversity of crAssphage strains in metagenomic samples
Fig. 3: Global locations of 2,424 crAssphage strains for amplicon A.
Fig. 4: Maximum likelihood phylogeny and dot plot showing full genomic colinearity between crAssphage and ten long contigs that were assembled from faecal metagenomes of different non-human primates.