Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Abstract

Metagenomic sequence analysis is rapidly becoming the primary source of virus discovery1,2,3. A substantial majority of the currently available virus genomes come from metagenomics, and some of these represent extremely abundant viruses, even if never grown in the laboratory. A particularly striking case of a virus discovered via metagenomics is crAssphage, which is by far the most abundant human-associated virus known, comprising up to 90% of sequences in the gut virome4. Over 80% of the predicted proteins encoded in the approximately 100 kilobase crAssphage genome showed no significant similarity to available protein sequences, precluding classification of this virus and hampering further study. Here we combine a comprehensive search of genomic and metagenomic databases with sensitive methods for protein sequence analysis to identify an expansive, diverse group of bacteriophages related to crAssphage and predict the functions of the majority of phage proteins, in particular those that comprise the structural, replication and expression modules. Most, if not all, of the crAss-like phages appear to be associated with diverse bacteria from the phylum Bacteroidetes, which includes some of the most abundant bacteria in the human gut microbiome and that are also common in various other habitats. These findings provide for experimental characterization of the most abundant but poorly understood members of the human-associated virome.

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Fig. 1: Architecture and evolution of the capsid gene module of the crAss-like phage family.
Fig. 2: Whole-genome maps of crAssphage and IAS virus, the two members of the crAss-like family that are abundant in the human gut virome.
Fig. 3: Replicative gene module of the crAss-like phage family.
Fig. 4: Genome expression gene module of the crAss-like phage family.

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Acknowledgements

The authors thank Y.I. Wolf and S. Shmakov for technical help and Koonin group members for discussion. N.Y., K.S.M., A.B.G. and E.V.K. are supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine).

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E.V.K. conceived of the study. N.Y., K.S.M. and M.K. performed research. N.Y., K.S.M., A.B.G., M.K., A.S., R.A.E. and E.V.K. analysed the data. E.V.K. wrote the manuscript, which was read, edited and approved by all authors.

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Correspondence to Eugene V. Koonin.

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Supplementary information

Supplementary information

Supplementary Figures 1–3 and Supplementary Notes 1 and 2.

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Supplementary Dataset 1

The selected representative set of crAss-like family members; conserved genes in the crAss-like phage family (an extended version of Table 1); BLAST scores of conserved crAss-like family proteins.

Supplementary Dataset 2

Annotation of the crAssphage and IAS phage genes and comparison of the MetaGeneMark and the current RefSeq (Glimmer) crAssphage annotations.

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Yutin, N., Makarova, K.S., Gussow, A.B. et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat Microbiol 3, 38–46 (2018). https://doi.org/10.1038/s41564-017-0053-y

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