A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

By Bas E. Dutilh, N. Cassman, Katelyn McNair, S. Sanchez, G. G. Silva, Lance Boling, J. Barr, D. Speth, V. Seguritan, Ramy Karam Aziz and 4 more. Nature Communications, 2014

713 citations recorded by the source corpus.

Metagenomics, or sequencing of the genetic material from a complete microbial community, is a promising tool to discover novel microbes and viruses. Viral metagenomes typically contain many unknown sequences. Here we describe the discovery of a previously unidentified bacteriophage present in the majority of published human faecal metagenomes, which we refer to as crAssphage. Its ~97 kbp genome is six times more abundant in publicly available metagenomes than all other known phages together; it comprises up to 90% and 22% of all reads in virus-like particle (VLP)-derived metagenomes and total community metagenomes, respectively; and it totals 1.68% of all human faecal metagenomic sequencing reads in the public databases. The majority of crAssphage-encoded proteins match no known sequences in the database, which is why it was not detected before. Using a new co-occurrence profiling approach, we predict a Bacteroides host for this phage, consistent with Bacteroides-related protein homologues and a unique carbohydrate-binding domain encoded in the phage genome. Metagenomic studies of microbial communities often report DNA sequences from unidentified viruses. Here, Dutilh et al. analyse metagenomic data to reveal the complete genome of an abundant, ubiquitous virus from human faeces, and predict that the virus infects bacteria of the Bacteroides group.

Subfields: Ecology, Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c98044cabe7d857f572336f8804ed52eaf05819f

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Citations in the corpus

Disease-specific Alterations in the Enteric Virome in Inflammatory Bowel Disease (2015, background): “We mapped a subset of our total VLP enriched sequences from the UK cohort to the recently discovered crAssphage genome and detected it in 71% of our samples (Dutilh et al., 2014) (Table S4).”
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation (2016, background): “After further examination, exceptions were made for four uncultured virus genomes obtained from metagenomic studies because these viruses have been validated experimentally (43,44,49).”
Molecular and Evolutionary Determinants of Bacteriophage Host Range. (2019, background): “First, viruses observed in environmental samples through epifluorescence microscopy [86] and metagenomic screens consistently showed that the majority of natural viruses remain uncharacterized [12,65].”
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome (2018, positive): “Metagenomic data also provide a means to quantify the abundance and relative distribution of genomes in environmental samples through read recruitment ( Tyson et al., 2004 ; Dutilh et al., 2014 ; Eren et al., 2015 ).”
NCBI Viral Genomes Resource (2014, background): “Whereas primary databases are archival repositories of sequence data, reference databases provide curated datasets that enable a number of activities, among them are transfer annotation to related genomes (11) (12) (13) , sequence assembly and virus discovery (14) (15) (16) (17) , viral dynamics and”
Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. (2019, background): “cant homology to any known bacteriophages, it was predicted to infect Bacteroides based on co-abundance and CRISPR spacer hits (Dutilh et al., 2014; Cinek et al., 2017).”
Identifying viruses from metagenomic data using deep learning (2020, result): “This is consistent with the fact that crAssphage is a highly abundant virus in healthy guts [42].”
Computational approaches to predict bacteriophage–host relationships (2015, background): “For example, we showed that up to 22% of the metagenomic sequencing reads in total community shotgun metagenomes may be derived from abundant bacteriophages like crAssphage (Dutilh et al. 2014).”
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses (2020, background): “Only two of these vOTUs included a reference genome: vOTU 043225 includes Faecalibacterium phage FP Mushu initially identified as a prophage in Faecalibacterium prausnitzii genomes and putatively associated with inflammatory bowel disease patients (46), while vOTU 002247 includes the ‘Uncultured crA”