A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

Espen, Lore Van; Bak, Emilie Glad; Beller, Leen; Close, Lila; Deboutte, Ward; Juel, Helene Bæk; Nielsen, Trine; Sinar, Deniz; Coninck, Lander De; Frithioff-Bøjsøe, Christine; Fonvig, Cilius Esmann; Jacobsen, Suganya; Kjærgaard, Maria; Thiele, Maja; Fullam, Anthony; Kuhn, Michael; Holm, Jens Christian; Bork, Peer; Krag, Aleksander; Hansen, Torben; Arumugam, Manimozhiyan; Matthijnssens, Jelle

doi:10.1128/msystems.00382-21

Cited by 35 publications

(64 citation statements)

References 115 publications

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“…Two of the most prevalent and abundant species were OTU-66229 and OTU-72541. These phages are highly similar to the recently described Bacteroides phages LoVEphage 37 and Hankyphage (p00) 57 , respectively (Supplementary Fig. 3).…”

Section: Resultssupporting

confidence: 79%

“…For example, the first representative of one of the most abundant bacteriophage clades - crAss-like viruses - was discovered only in 2014 56 . Similar examples, such as the highly prevalent Hankyphage (p00) 57 and LoVEphage 37 , were discovered only in 2018 and 2021, respectively. We anticipate that Phanta, when applied with its default database, will allow similar key discoveries to be made.…”

Section: Discussionmentioning

confidence: 84%

“…However, despite their strengths at de novo phage discovery, assembly-based approaches have limited ability to detect low-abundance phages, due to the relative difficulty of assembling the genomes of low abundance taxa [28][29][30] . With increases in shotgun metagenomes from human gut samples, more comprehensive databases of gut viral genomes have recently been created 27,[31][32][33][34][35][36][37] . By using these new compendiums, it is now possible to profile gut viruses and their prokaryotic hosts simultaneously through read-based, reference-dependent methods.…”

Section: Introductionmentioning

confidence: 99%

“…With increases in shotgun metagenomes from human gut samples, more comprehensive databases of gut viral genomes have recently been created 27,31–37 . By using these new compendiums, it is now possible to profile gut viruses and their prokaryotic hosts simultaneously through read-based, reference-dependent methods.…”

Section: Introductionmentioning

confidence: 99%

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Phanta: Phage-inclusive profiling of human gut metagenomes

Pinto

Chakraborty

Jain

et al. 2022

Preprint

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The human gut microbiome is a diverse ecosystem that encompasses multiple domains of life and plays a vital role in human health. Due to technical limitations, most microbiome studies have focused on gut prokaryotes, overlooking bacteriophages and other gut viruses. The most common method to profile viruses is to assemble shotgun metagenomic reads - often from virus-enriched samples - and identify viral genomes de novo. While valuable, this resource-intensive and reference-independent method has limited sensitivity. To overcome these drawbacks, we developed Phanta, which profiles human gut metagenomes in a virus-inclusive manner directly from short reads utilizing recently published catalogs of gut viral genomes. Phanta incorporates k-mer based classification tools and was developed with virus-specific properties in mind. Specifically, it includes optimizations considering viruses' small genome size, sequence homology with prokaryotes, and interactions with other members of the gut microbial community. Based on simulations, the workflow is fast and accurate with respect to both prokaryotes and viruses, minimizing false positive species identification using a novel genome coverage-based strategy. When applied to metagenomes from healthy adults, Phanta identified ~200 viral species per sample, ~5x more than the standard assembly-based methods. Notably, we observed a 2:1 ratio between gut viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. Phanta performs equally well on bulk vs. virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis. Phanta can tandemly profile gut viruses and prokaryotes in existing and novel datasets, and can therefore identify cross-domain interactions with likely relevance to human health. We expect that Phanta will reduce the barrier to virus-inclusive studies of the human gut microbiome, thus making it standard practice.

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Section: Resultssupporting

confidence: 79%

Section: Discussionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phanta: Phage-inclusive profiling of human gut metagenomes

Pinto

Chakraborty

Jain

et al. 2022

Preprint

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“…The gut viromes are studied using the in-house developed NetoVIR protocol [ 95 ] and a combination of optimized bioinformatic tools. A first aim of the project was to develop a viral genome catalog (DEVoC), that led to the identification of a previously undescribed prevalent phage [ 96 ]. Currently, her major focus point is to study the interaction between phages and their bacterial hosts.…”

Section: Women In the Evbcmentioning

confidence: 99%

Women in the European Virus Bioinformatics Center

Hufsky

Abecasis

Patrícia

et al. 2022

Viruses

Self Cite

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Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing “Big Data” offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.

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Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing

Chen,

Sun,

Dong

et al. 2024

Advanced Science

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Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus‐like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short‐ and long‐read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non‐redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short‐read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long‐read or hybrid assemblies, with little overlap with those assembled from only the short‐read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral‐host interaction network to facilitate future research and applications.

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A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog

Cited by 35 publications

References 115 publications

Phanta: Phage-inclusive profiling of human gut metagenomes

Phanta: Phage-inclusive profiling of human gut metagenomes

Women in the European Virus Bioinformatics Center

Efficient Recovery of Complete Gut Viral Genomes by Combined Short‐ and Long‐Read Sequencing

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