REFERENCES
1. Shkoporov AN, Hill C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe. 2019;25:195-209.
2. Pargin E, Roach MJ, Skye A, et al. The human gut virome: composition, colonization, interactions, and impacts on human health. Front. Microbiol. 2023;14:963173.
3. Dutilh BE, Cassman N, Mcnair K, et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat Commun. 2014;5:4498.
4. Guerin E, Shkoporov A, Stockdale SR, et al. Biology and taxonomy of crAss-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe. 2018;24:653-664.e6.
5. Bin Jang H, Bolduc B, Zablocki O, et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat Biotechnol. 2019;37:632-9.
6. Bolduc B, Zablocki O, Turner D, et al. Machine learning enables scalable and systematic hierarchical virus taxonomy. Nat Biotechnol. 2025:2946.
7. Yang F, Xiong L, Li M, et al. A signature-protein-based approach for accurate and efficient profiling of the human gut virome. Cell Rep Methods. 2026;6:101250.
8. Liu H, Shen J, Zhang Z, et al. Exploring functional insights into the human gut microbiome via the structural proteome. Cell Host Microbe. 2026;34:167-185.e9.
9. Tal N, Hadary R, Chang RB, et al. Structural modeling reveals phage proteins that manipulate bacterial immune signaling. Science. 2026;391:eaea1761.
10. Shkoporov AN, Stockdale SR, Lavelle A, et al. Viral biogeography of the mammalian gut and parenchymal organs. Nat Microbiol. 2022;7:1301-11.
11. Shkoporov AN, Clooney AG, Sutton TD, et al. The human gut virome is highly diverse, stable, and individual specific. Cell Host Microbe. 2019;26:527-541.e5.
12. Shkoporov AN, Khokhlova EV, Fitzgerald CB, et al. ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat Commun. 2018;9:4781.
13. Bayfield OW, Shkoporov AN, Yutin N, et al. Structural atlas of a human gut crassvirus. Nature. 2023;617:409-16.
14. Shkoporov AN, Khokhlova EV, Stephens N, et al. Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis. BMC Biol. 2021;19:163.
15. Cortés-Martín A, Buttimer C, Maier JL, et al. Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages. Gut Microbes. 2025;17:2507775.
16. Porter NT, Canales P, Peterson DA, Martens EC. A subset of polysaccharide capsules in the human symbiont Bacteroides thetaiotaomicron promote increased competitive fitness in the mouse gut. Cell Host Microbe. 2017;22:494-506.e8.
17. Borodovich T, Shkoporov AN, Ross RP, Hill C. Phage-mediated horizontal gene transfer and its implications for the human gut microbiome. Gastroenterol Rep. 2022;10:goac012.
18. Borodovich T, Buttimer C, Wilson JS, et al. Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome. Nat Commun. 2026;17:2046.






