What the Phage: A scalable workflow for the identification and analysis of phage sequences

Marquet, Mike; Hölzer, Martin; Pletz, Mathias W.; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, Christian

doi:10.1101/2020.07.24.219899

Cited by 14 publications

(16 citation statements)

References 35 publications

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“…The identified contigs from each assembly were then compiled and clustered at 95% nucleotide identity using CD-HIT v4.8.1 (parameters: -c 0.95 -d 400 -T 20 -M 20000 -n 5) [44], producing 2,885 viral OTUs (vOTUs). Viral contigs identified by (3) were further validated using "What the Phage" (WtP) [45] and VIBRANT (v1.2.1, virome mode) [46], both with default settings. WtP v1.0.0 combines 12 established viral identification tools for the identification and analysis of viral sequences.…”

Section: Identification Of Viral Contigsmentioning

confidence: 99%

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

et al. 2021

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In marine ecosystems, viruses exert control on the composition and metabolism of microbial communities, influencing overall biogeochemical cycling. Deep sea sediments associated with cold seeps are known to host taxonomically diverse microbial communities, but little is known about viruses infecting these microorganisms. Here, we probed metagenomes from seven geographically diverse cold seeps across global oceans to assess viral diversity, virus–host interaction, and virus-encoded auxiliary metabolic genes (AMGs). Gene-sharing network comparisons with viruses inhabiting other ecosystems reveal that cold seep sediments harbour considerable unexplored viral diversity. Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition. In silico predictions linked 14.2% of the viruses to microbial host populations with many belonging to poorly understood candidate bacterial and archaeal phyla. Lysis was predicted to be a predominant viral lifestyle based on lineage-specific virus/host abundance ratios. Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling via virus-induced mortality and/or metabolic augmentation. Overall, these findings reveal the global diversity and biogeography of cold seep viruses and indicate how viruses may manipulate seep microbial ecology and biogeochemistry.

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Section: Identification Of Viral Contigsmentioning

confidence: 99%

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

et al. 2021

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“…To support a transparent and reproducible metagenomics workflow, all reads that cannot be mapped back to the existing high-quality bins (after the refinement) are available as an output for further analysis. These "unused" reads could be further analyzed by other tools such as Kraken2 [ 40 ], Kaiju [ 41 ], or centrifuge [ 42 ] for read classification, "What the Phage" [ 43 ] to search for phages, mi-faser [ 44 ] for functional annotation of the reads or even use these reads as a new input to run MUFFIN.…”

Section: Introductionmentioning

confidence: 99%

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

et al. 2021

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Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction. However, the integration of two different sequencing modalities makes downstream analyses complex. We, therefore, developed MUFFIN, a complete metagenomic workflow that uses short and long reads to produce high-quality bins and their annotations. The workflow is written by using Nextflow, a workflow orchestration software, to achieve high reproducibility and fast and straightforward use. This workflow also produces the taxonomic classification and KEGG pathways of the bins and can be further used for quantification and annotation by providing RNA-Seq data (optionally). We tested the workflow using twenty biogas reactor samples and assessed the capacity of MUFFIN to process and output relevant files needed to analyze the microbial community and their function. MUFFIN produces functional pathway predictions and, if provided de novo metatranscript annotations across the metagenomic sample and for each bin. MUFFIN is available on github under GNUv3 licence: https://github.com/RVanDamme/MUFFIN.

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“…The same procedure was employed against the mMGE and GPD databases (44,51). Further, phage prediction using the genomic neighborhood information was performed using the upstream and downstream nucleotide sequences (+-10kb) of every representative sequence as a query for the metasoftware WhatThePhage (52). Only sequences predicted to be encoded in phages/prophages by at least 3 different tools included in WhatThePhage were labeled as so.…”

Section: Methodsmentioning

confidence: 99%

“…In addition, UG15 members have been also found within the Helicobacter pylori accessory genome (HPSJM_07740 gene of H. pylori SJM180) (92). To find which UG/Abi RTs were encoded in MGEs, we analyzed the genomic context of every representative sequence in search of phage signatures using the metasoftware WhatThePhage (52) and searched MGE databases (50) with all prokaryotic RTs HMM profiles (Methods).…”

Section: Presence Of Ug/abi Rts In Mobile Genetic Elements and Viral Genomesmentioning

confidence: 99%

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

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Gao

Shah

et al. 2021

Preprint

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Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

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What the Phage: A scalable workflow for the identification and analysis of phage sequences

Cited by 14 publications

References 35 publications

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

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