Metaviromics coupled with phage-host identification to open the viral ‘black box’

Moon, Kira; Cho, Jang-Cheon

doi:10.1007/s12275-021-1016-9

Cited by 12 publications

(14 citation statements)

References 142 publications

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“…In total, we obtained 89 MAGs with ≥ 70% completion and ≤10% contamination that were used for host-prediction (Table S3). Considering the intrinsic challenges of in silico host prediction (Khot, Strous & Hawley, 2020; Moon & Cho, 2021) a scoring matrix was developed to combine the results from prophage blast, tRNA scan, and WIsH to improve the accuracy of host assignments. Despite this, only six out of 2,301 viral populations (0.26%) were successfully linked to three hosts which belonged to the phylum of Actinobacteriota (n = 2) and Chloroflexota (n = 1).…”

Section: Resultsmentioning

confidence: 99%

Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea

Warwick-Dugdale

Tian

Michelsen

et al. 2022

Preprint

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In the summer months, the waters of the Sargasso Sea are nutrient-limited and strongly stratified, serving as a model system for the predicted warmer and nutrient limited oceans of the Anthropocene. The dominant microorganisms of surface waters are key drivers of the global carbon cycle. However, the viruses of the Sargasso Sea that shape these host communities and influence host biogeochemical function are not well understood. Here, we apply a hybrid sequencing approach that combines short- and long reads to survey Sargasso Sea phage communities via metagenomics at the viral maximum (80m) and mesopelagic (200m) depths. Taxonomically, we identified 2,301 Sargasso Sea phage populations (~species-level taxonomy) across 186 genera. Over half of the phage populations lacked representation in other global ocean viral metagenomes, whilst 177 phage genera lacked representation in phage isolate databases. Viral fraction and cell associated viral communities captured in short-read data were distinct and decoupled at both depths, possibly indicating low active lytic viral replication in the Sargasso Sea, with viral turnover occurring across periods longer than the sampling period of three days. Inclusion of long read data was critical for (1) the identification of 79 ecologically important and common viral genomes; (2) capturing the extent of viral genome microdiversity; and (3) enabling the recovery of hypervariable regions in viral genomes predicted to encode proteins involved in host recognition, DNA synthesis and DNA packaging. Host prediction was only possible for ~4% of viral populations. Genomes of phages known to infect Prochlorococcus and Pelagibacter were poorly represented in our data, supporting recent evidence of low infection levels in the dominant bacterial taxa of oligotrophic regions.

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Section: Resultsmentioning

confidence: 99%

Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea

Warwick-Dugdale

Tian

Michelsen

et al. 2022

Preprint

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“…It is known that the vast majority of bacteria are not culturable [79]; however, the high-throughput sequencing technology combined with bioinformatics analysis methods enabled us to recruit a large number of complete genomes, the so-called metagenome-assembled genomes of not-yet-cultured bacteria or phages [80][81][82]. Due to the high diversity and lack of conserved marker genes, the taxonomy of phages remains a big challenge.…”

Section: Discussionmentioning

confidence: 99%

Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

Yang

Zhang

et al. 2022

Microbiome

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Background As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. Results Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. Conclusions We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth.

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“…This may therefore bias the accuracy of bacterial host prediction. Another issue is that some phages can potentially be missed during virus-particle filtration, resulting in a biased representation of phage abundance and their associated hosts [ 7 , 36 ]. A final challenge is that the ability to classify phage sequences, whether to identify the taxa present or the putative functionality of a coding region, depends on the availability of representative viral sequences in the data repository used [ 37 ].…”

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…In recent decades, shotgun metagenomic sequencing has been proposed to study genomes of uncultured viral populations in the environment, an approach known as viral metagenomics [ 7 ]. This has allowed virome analysis (of all viral assemblies in a given environment) to uncover many new phage genomes never previously reported, enriching viral sequence databases [ 7 ]. However, in contrast to the conventional culture-based approach, which provides direct host information, viral metagenomics does not reveal the relationships between phages and their hosts [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

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Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Andrianjakarivony

Bettarel

Armougom

et al. 2022

Viruses

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Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage–host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages’ bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.

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Metaviromics coupled with phage-host identification to open the viral ‘black box’

Cited by 12 publications

References 142 publications

Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea

Long-read powered viral metagenomics in the Oligotrophic Sargasso Sea

Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

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