ArticleNucleic acids research2021
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers, 1 of them a synthesis that pooled it.
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Who cites it
76 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease.Gut microbes · 2026Review
- Phage Genomics and Bioinformatics in Therapeutic Development: Evidence Limits, Validation Gates, and Translational Decision-Making.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Bacteriophages as Phagobiotics: Scientific Rationale and Translational Boundaries for Gut Microbiome Modulation.Viruses · 2026Review
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Genomic landscape of 340 virulent Acinetobacter bacteriophages reveals anti-CRISPR-enriched candidates for therapeutic prioritization.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2026Article
- Computational tool choice impacts CRISPR spacer-protospacer detection.Bioinformatics (Oxford, England) · 2026Article
- A diverse gut virome in natural populations of Drosophila melanogaster.Animal microbiome · 2026Article
- Understanding the probiotic potential of a healthy human vaginal flora, Lactobacillus gasseri K9: genomic and in vitro aspects.Journal, genetic engineering & biotechnology · 2026Article
- Review
- Phage satellites induced by virulent phages are mobilized by natural competence leading to phage resistance in a new host.Nature communications · 2026Article
- RuSpacer: a CRISPR spacer database derived from ruminant-associated prokaryotes for virome analysis.Scientific reports · 2026Article
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- Molecular kinetics dictate population dynamics in CRISPR-based plasmid defense.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- High-resolution phage-host assignment through key proteins using large language models.Nature communications · 2026Article
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
- Abundance-activity decoupling in sulfur-cycling bacteria reflects viral infection types in meromictic lakes.The ISME journal · 2026Article
- CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated withJournal of oral microbiology · 2026Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Thousands of new phages have recently been discovered thanks to viral metagenomics. These phages are extremely diverse and their genome sequences often do not resemble any known phages. To appreciate their ecological impact, it is important to determine their bacterial hosts. CRISPR spacers can be used to predict hosts of unknown phages, as spacers represent biological records of past phage-bacteria interactions. However, no guidelines have been established to standardize host prediction based on CRISPR spacers. Additionally, there are no tools that use spacers to perform host predictions on large viral datasets. Here, we developed a set of tools that includes all the necessary steps for predicting the hosts of uncharacterized phages. We created a database of >11 million spacers and a program to execute host predictions on large viral datasets. Our host prediction approach uses biological criteria inspired by how CRISPR-Cas naturally work as adaptive immune systems, which make the results easy to interpret. We evaluated the performance using 9484 phages with known hosts and obtained a recall of 49% and a precision of 69%. We also found that this host prediction method yielded higher performance for phages that infect gut-associated bacteria, suggesting it is well suited for gut-virome characterization.
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