ArticleGenome research2012
CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers, 1 of them a synthesis that pooled it.
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Who cites it
119 citing papers in PubMed, 1 synthesis or guideline pooled it, 223 citations in OpenAlex.
- Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies.Briefings in bioinformatics · 2024Pooled it
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- Effect of bacteriophages on growth performance and health indicators in broiler chickens in the absence of bacterial challenge - A review.Veterinarni medicina · 2026Review
- Identification and comparative genomic analysis of prophage sequences and CRISPR‒Cas immunity in Methylococcus genomes: insights into industrial methane bioconversion.Biotechnology for biofuels and bioproducts · 2026Article
- Cytokines Meet Phages: A Revolutionary Pathway to Modulating Immunity and Microbial Balance.Biomedicines · 2025Review
- Antimicrobial resistance: use of phage therapy in the management of resistant infections.Molecular biology reports · 2024Review
- Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits.Microbiome · 2024Article
- PB-LKS: a python package for predicting phage-bacteria interaction through local K-mer strategy.Briefings in bioinformatics · 2024Article
- Dynamics of CRISPR-mediated virus-host interactions in the human gut microbiome.The ISME journal · 2024Article
- Genomic and functional analysis of the mucinolytic speciesFrontiers in microbiology · 2024Article
- Prophage Carriage and Genetic Diversity within Environmental Isolates ofInternational journal of molecular sciences · 2023Article
- Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases.JHEP reports : innovation in hepatology · 2023Review
- Gut Phageome-An Insight into the Role and Impact of Gut Microbiome and Their Correlation with Mammal Health and Diseases.Microorganisms · 2023Review
- Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning.Briefings in bioinformatics · 2023Article
- Critical Signaling Transduction Pathways and Intestinal Barrier: Implications for Pathophysiology and Therapeutics.Pharmaceuticals (Basel, Switzerland) · 2023Review
- The Outer Membrane Cytochrome OmcA Is Essential for Infection of Shewanella oneidensis by a Zebrafish-Associated Bacteriophage.Journal of bacteriology · 2023Article
- Prophage-Derived Regions inInternational journal of molecular sciences · 2023Article
- Morphological and Genetic Characterization ofViruses · 2022Article
- Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-ResistantmSystems · 2022Article
59 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The bacterial community in the human gut has crucial health roles both in metabolic functions and in protection against pathogens. Phages, which are known to significantly affect microbial community composition in many ecological niches, have the potential to impact the gut microbiota, yet thorough characterization of this relationship remains elusive. We have reconstructed the content of the CRISPR bacterial immune system in the human gut microbiomes of 124 European individuals and used it to identify a catalog of 991 phages targeted by CRISPR across all individuals. Our results show that 78% of these phages are shared among two or more individuals. Moreover, a significant fraction of phages found in our study are shown to exist in fecal samples previously derived from American and Japanese individuals, identifying a common reservoir of phages frequently associated with the human gut microbiome. We further inferred the bacterial hosts for more than 130 such phages, enabling a detailed analysis of phage-bacteria interactions across the 124 individuals by correlating patterns of phage abundance with bacterial abundance and resistance. A subset of phages demonstrated preferred association with host genomes as lysogenized prophages, with highly increased abundance in specific individuals. Overall, our results imply that phage-bacterial attack-resistance interactions occur within the human gut microbiome, possibly affecting microbiota composition and human health. Our finding of global sharing of gut phages is surprising in light of the extreme genetic diversity of phages found in other ecological niches.
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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.