Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein

Papudeshi, B.; Vega, A. A.; Souza, C.; Giles, S. K.; Mallawaarachchi, V.; Roach, M. J.; An, M.; Jacobson, N.; McNair, K.; Mora, M. F.; Pastrana, K.; Leigh, C.; Cram, C.; Plewa, W. S.; Grigson, S. R.; Bouras, G.; Decewicz, P.; Luque, A.; Droit, L.; Handley, S. A.; Segall, A.; Dinsdale, E. A.; Edwards, R. A.

doi:10.1101/2023.03.05.531146

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bioRxiv · 10.1101/2023.03.05.531146

Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein

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Abstract

Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to the Crassvirales order. Despite identifying over 600 Crassvirales genomes computationally, only few have been successfully isolated. Continued efforts in isolation of more Crassvirales genomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting various Bacteroides hosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novel Crassvirales species infecting Bacteroides cellulosilyticus WH2. These species, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully cultured Crassvirales species and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present three Crassvirales species as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome. Impact statementBacteriophages play a crucial role in shaping microbial communities within the human gut. Among the most dominant bacteriophages in the human gut microbiome are Crassvirales phages, which infect Bacteroides. Despite being widely distributed, only a few Crassvirales genomes have been isolated, leading to a limited understanding of their biology, ecology, and evolution. This study isolated and characterized three novel Crassvirales genomes belonging to two different families, and three genera, but infecting one bacterial host, Bacteroides cellulosilyticus WH2. Notably, the observation confirmed the phages are not co-evolving with their bacterial hosts, rather have a shared ability to exploit similar features in their bacterial host. Additionally, the identification of a critical viral protein undergoing purifying selection and interacting with the bacterial receptors opens doors to targeted therapies against bacterial infections. Given Bacteroides role in polysaccharide degradation in the human gut, our findings advance our understanding of the phage-host interactions and could have important implications for the development of phage-based therapies. These discoveries may hold implications for improving gut health and metabolism to support overall well-being. Data summaryThe genomes used in this research are available on Sequence Read Archive (SRA) within the project, PRJNA737576. Bacteroides cellulosilyticus WH2, Kehishuvirus sp. tikkala strain Bc01, Kolpuevirus sp. frurule strain Bc03, and Rudgehvirus jaberico strain Bc11 are all available on GenBank with accessions NZ_CP072251.1 (B. cellulosilyticus WH2), QQ198717 (Bc01), QQ198718 (Bc03), and QQ198719 (Bc11), and we are working on making the strains available through ATCC. The 3D protein structures for the three Crassvirales genomes are available to download at doi.org/10.25451/flinders.21946034.

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Papudeshi, B., Vega, A. A., Souza, C., Giles, S. K., Mallawaarachchi, V., Roach, M. J., An, M., Jacobson, N., McNair, K., Mora, M. F., Pastrana, K., Leigh, C., Cram, C., Plewa, W. S., Grigson, S. R., Bouras, G., Decewicz, P., Luque, A., Droit, L., Handley, S. A., Segall, A., Dinsdale, E. A., Edwards, R. A.. 2023-03-06. Novel crAssphage isolates exhibit conserved gene order and purifying selection of the host specificity protein. https://doi.org/10.1101/2023.03.05.531146

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