ArticleBacteriophage
Metagenomic ventures into outer sequence space.
Article in Bacteriophage. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.Zoological research · 2026Article
- Mini review: antimicrobial compounds produced by bacteria associated with marine invertebrates.Folia microbiologica · 2025Review
- MetaAll: integrative bioinformatics workflow for analysing clinical metagenomic data.Briefings in bioinformatics · 2024Article
- Bacteriophages: a double-edged sword in the gastrointestinal tract.Frontiers in microbiomes · 2024Review
- Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.Nature communications · 2021Article
- Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT.Genome biology · 2019Article
- Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis.Virology journal · 2018Article
- Discovering viral genomes in human metagenomic data by predicting unknown protein families.Scientific reports · 2018Article
- Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut.Nature microbiology · 2018Article
- Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans.Nature communications · 2017Article
- Stable core virome despite variable microbiome after fecal transfer.Gut microbes · 2017Review
- Computational approaches to predict bacteriophage-host relationships.FEMS microbiology reviews · 2016Review
- Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane OxidizingFrontiers in microbiology · 2016Article
- From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.Cellular and molecular life sciences : CMLS · 2015Review
- Beyond research: a primer for considerations on using viral metagenomics in the field and clinic.Frontiers in microbiology · 2015Article
Corrections and comments
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Authors and funding
1 author.
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Abstract
Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as "unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as "biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.