ArticleNature biotechnology2024
Phage-inclusive profiling of human gut microbiomes with Phanta.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.Cell reports. Medicine · 2025Trial
- Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.Nature genetics · 2026Article
- Remodelling of the gut virome after long-term fasting.NPJ biofilms and microbiomes · 2026Article
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- The Unified Human Virome Database: A toolkit for expanded human virome analysis.bioRxiv : the preprint server for biology · 2026Article
- The effects of bacteriophage cocktail treatment on healthy gut microbiota: anMicrobial genomics · 2026Article
- Gut virome-microbiome interactions across hosts and environments.NPJ biofilms and microbiomes · 2026Article
- Dysbiosis of fecal virome in pediatric Crohn's disease and its dynamic changes during infliximab therapy.mSystems · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.Microbiome · 2026Article
- Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.bioRxiv : the preprint server for biology · 2026Article
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
- Article
- Species-level virome profiling reveals compositional differences in the gut prokaryotic DNA virome of people with HIV-1 on antiretroviral therapy.Gut microbes reports · 2026Article
- Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.Journal of cachexia, sarcopenia and muscle · 2026Article
- Bacteriophage-driven DNA inversions shape bacterial functionality and long-term co-existence inGut microbes · 2025Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.Cell host & microbe · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.
Indexed as
Identifiers
37231259What OpenQuestion holds
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.