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Host diversity slows bacteriophage adaptation by selecting generalists over specialists

Abstract

Most viruses can infect multiple hosts, yet the selective mechanisms that maintain multi-host generalists over single-host specialists remain an open question. Here we propagate populations of the newly identified bacteriophage øJB01 in coculture with many host genotypes and find that while phage can adapt to infect any of the new hosts, increasing the number of hosts slows the rate of adaptation. We quantify trade-offs in the capacity for individual phage to infect different hosts and find that phage from evolved populations with more hosts are more likely to be generalists. Sequencing of evolved phage reveals strong selection and the genetic basis of adaptation, supporting a model that shows how the addition of more potential hosts to a community can select for low-fitness generalists over high-fitness specialists. Our results show how evolution with multiple hosts alters the rate of viral adaptation and provides empirical support for an evolutionary mechanism that promotes generalists over specialists.

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Fig. 1: Adaptation of the novel phage øJB01 to a community of permissive and non-permissive E. coli hosts.
Fig. 2: Increased host diversity slows phage adaptation.
Fig. 3: Evolution with multiple hosts is shaped by trade-offs for infectivity on each host.
Fig. 4: Host identity and host diversity impacts the evolution of generalists.
Fig. 5: Parallel evolution of the tail fibre protein gp17.
Fig. 6: Community diversity and trade-offs predict the relative fitness of generalists and specialists.

Data availability

Raw sequencing reads used to generate the data in Fig. 4a and Extended Data Fig. 4 have been deposited in GenBank under the Bioproject ID PRJNA673261.

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Acknowledgements

M.J.M. was supported by ARC Discovery Grant (grant no. DP180102161) and ARC Future Fellowship (grant no. FT170100441).

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Contributions

M.J.M. undertook the conceptualization, methodology, resources and funding acquisition. M.J.M. and J.J.B. supervised the work. M.J.M. and D.G.S. were responsible for project administration. M.J.M. and D.G.S. conducted the formal analysis. M.J.M., D.G.S. and J.J.B. undertook validation of results. D.G.S. was involved in investigation and visualization. L.C.W. provided software and data curation. M.J.M. and D.G.S. prepared the original draft manuscript. J.J.B. then reviewed and edited the manuscript.

Corresponding author

Correspondence to Michael J. McDonald.

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The authors declare no competing interests.

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Peer review information Nature Ecology & Evolution thanks Britt Koskella and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Growth of E. coli EPEC and phage øJB01 in coculture.

The number of øJB01 plaque-forming units were monitored over a period of 90 min in coculture with exponential phase E. coli EPEC at MOI 0.1(A). The growth of E. coli EPEC was assayed using a plate reader. E. coli EPEC was propagated either in monoculture, or in coculture with phage øJB01 added at two different MOIs (1 and 0.1) (B). Error bars represent standard error of the mean (SEM) (n = 3).

Extended Data Fig. 2 Two-way plots showing data used for simplex plots in Fig. 4.

Panels a-c correspond to three-host treatment (EPEC, MG1655, BL21). Panels d-f correspond to the three-host treatment (EPEC, MG1655, REPEC). Measurements of infectivity (PFU) for phage clones isolated from MG1655 (blue circles), EPEC (orange triangles), BL21(red squares) and REPEC (green diamonds). Filled markers show the measurements for phage clones obtained at the end point of the experiment (Day 10). Open markers show phage clones sampled at early timepoints (day 4 - day 9). Error bars are SEM, n = 3.

Extended Data Fig. 3 CLUSTAL multiple sequence alignment of tail fibre protein gp17.

The amino acid sequence of Escherichia øJB01 phage, gp17 was aligned with homologous sequences from Escherichia phage N30 and T7 phage. Identical amino acids are marked with asterisks and non-identical are marked by dots. The gp17 conserved region is from position 1- 250 and the hypervariable region from 300–554.

Extended Data Fig. 4 Phylogenetic tree based on the gp17 sequences of 26 phage clones from the three-host treatment (EPEC, MG1655, REPEC).

Sequences were aligned with MUSCLE (v3.8.31) in MEGA X51,52. The phylogenetic tree was reconstructed using the maximum likelihood method as implemented in PhyML (v3.1/3.0)53,54. The WAG substitution model55 was selected assuming an estimated proportion of invariant sites (of 0.951) and 4 gamma-distributed rate categories to account for rate heterogeneity across sites. The gamma shape parameter was estimated directly from the data (gamma=91.073). Reliability of internal branches was assessed using the aLRT test (SH-Like). Final Log-Liklihood: −1839.18. Phage clones labelled by phenotype and day of generation. ‘S’ or ‘G’ refers to specialist or generalist according to phenotypic measurements (Figs. 34) and the number refers to the day of isolation. C8, D8, C9, D9, E8, F8 refer to the specific three-host experimental population from which the phage clone was isolated. Each phage clone was obtained by plating the whole population lysate onto an individual host (Figs. 34). The strain name refers to that host of isolation. For example, ‘G10 C8 MG1655’ refers to a phage clone with a generalist phenotype isolated from a day 10 population C8, isolated from a plaque on MG1655. Numbers on branches show bootstrapping support for that branch (percent, 100 bootstraps). Strains are clustered based on those clades with greater than 80% support. Dashed lines are for labels and are not part of the tree.

Supplementary information

Supplementary Information

Supplementary Tables 1–7.

Reporting Summary

Supplementary Data

The genetic variants discovered in gp17 in all sequenced clones. For example, Day 4, Generalist, C8 REPEC is a clone that originated from Day 4 of the evolution experiment in the ‘C8’ replicate population within the three-host treatment with EPEC, MG1655 and REPEC. The clone itself was isolated as a plaque from a lawn of E. coli REPEC on an agar plate.

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Sant, D.G., Woods, L.C., Barr, J.J. et al. Host diversity slows bacteriophage adaptation by selecting generalists over specialists. Nat Ecol Evol 5, 350–359 (2021). https://doi.org/10.1038/s41559-020-01364-1

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