crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes

Brown, Bryan P.; Chopera, Denis; Havyarimana, Enock; Wendoh, Jerome; Jaumdally, Shameem Z.; Nyangahu, Donald D.; Gray, Clive M.; Martin, Darren P.; Varsani, Arvind; Jaspan, Heather B.

doi:10.1016/j.virusres.2020.198219

Cited by 11 publications

(11 citation statements)

References 33 publications

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“…Very few representatives of the order have been isolated in culture. The majority of species have been described based on analysis of metagenomically assembled genomes (MAGs) extracted from gut-associated, soil, marine, and industrial environments [15][16][17][18]. Members of the order Crassvirales are especially prevalent in mammalian gut microbiomes and were isolated from, or predicted to infect, bacteria of the phylum Bacteroidota (more specifically, order Bacteroidales in the mammalian gut) [19][20][21].…”

Section: Order Crassviralesmentioning

confidence: 99%

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

et al. 2023

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This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021−March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

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Section: Order Crassviralesmentioning

confidence: 99%

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

et al. 2023

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“…The known viral diversity of dsDNA-tailed phages has bloomed in recent years due to the increasing availability of shotgun metagenomic and metaviromic data, improved virome analysis pipelines, sensitive protein homology search tools, and expanding collections of reference genomes [ 7 , 9 , 105 ]. The range of known crAss-like phages has expanded from a few “orphan” species into the expansive and highly diverse new viral order of Crassvirales [ 8 , 46 ]. Still, the phylogeny of the Crassvirales and their evolutionary relationships with other dsDNA viruses remain largely unexplored.…”

Section: Discussionmentioning

confidence: 99%

“…An analysis of nucleotide polymorphisms and the rate of non-synonymous to synonymous changes (dN/dS) in crAssphage genomes from a mother-child cohort with low interpersonal viral diversity showed rapid evolution and strong positive selection for mutations in genes coding for RNAP and tail proteins [ 46 ]. Considering the crucial role tail proteins have in bacterial host recognition and the overcoming of acquired phage resistance, it is fitting that their genes would be targets of active selection.…”

Section: Co-evolution With Bacterial Hostsmentioning

confidence: 99%

“…(iii) Antagonistic co-evolution and the cost of resistance: a number of theoretical frameworks are often employed to describe phage-bacteria co-evolution, such as the “arms race” dynamics (resistance mutations in the host followed by host range counter-mutations in the phage) and “fluctuating selection” dynamics (Red Queen evolution), the latter leading to diversification of bacterial and phage populations [ 42 , 101 , 103 , 104 ]. Longitudinal observations show evidence that selective pressure driving evolution of crAss-like phage genes is particularly strong for tail components (including RBPs), indicating an arms race/Red Queen type of dynamics between phages and their hosts [ 13 , 46 , 88 ].…”

Section: Crassvirales Life Cycles and Phage-host Dynamics In...mentioning

confidence: 99%

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Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?

et al. 2023

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The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.

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“…This recently discovered bacteriophage infects Bacteroides intestinalis [28,29], and was found to be one of the most abundant human gut phages. In addition to human feces, CrAssphage has been detected in non-human primates and several mammal fecal samples [28,[30][31][32][33][34][35][36]. Due to its correlation with fecal material, its presence was suggested as a potential marker for fecal contamination [30,32,[37][38][39].…”

Section: Discussionmentioning

confidence: 99%

Virome Characterization in Commercial Bovine Serum Batches—A Potentially Needed Testing Strategy for Biological Products

Paim

Maggioli

Falkenberg

et al. 2021

Viruses

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Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies’ established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.

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crAssphage genomes identified in fecal samples of an adult and infants with evidence of positive genomic selective pressure within tail protein genes

Cited by 11 publications

References 33 publications

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?

Virome Characterization in Commercial Bovine Serum Batches—A Potentially Needed Testing Strategy for Biological Products

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