ArticleGut microbes
A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology.
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Fecal filtrate transplantation as salvage therapy for fulminantGut microbes · 2026Trial
- Targeting the human gut microbiome: a comparative review of probiotics, prebiotics, synbiotics, and postbiotics.Journal of advanced research · 2026Review
- Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.Probiotics and antimicrobial proteins · 2026Review
- Comprehensive Evaluation of Safety and Probiotic Potential of Lactiplantibacillus plantarum HY7715 Isolated from Korean kimchi.Probiotics and antimicrobial proteins · 2026Article
- Frequent Sweetened Beverage Consumption Is Associated With Accelerated Biological Aging: Evidence From a Population-Based Study and Gut Microbiota Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.bioRxiv : the preprint server for biology · 2026Article
- Lactiplantibacillus plantarum SLpl116 attenuates OVA-induced food allergy with ecological restoration of the gut microbiota and immune rebalancing.NPJ science of food · 2026Article
- Genome-Informed Characterization of Lactiplantibacillus plantarum ND88 with Inhibitory Activity against Representative Oral Pathogens.Probiotics and antimicrobial proteins · 2026Article
- Genomic evidence of ecological flexibility and cross-niche CRISPR spacerome targeting phage-plasmid hybrids in Latilactobacillus curvatus.BMC genomics · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Whole-genome sequencing reveals hidden antimicrobial resistance genes in phenotypically susceptible probiotic candidate lactic acid bacteria.Scientific reports · 2026Article
- Comparative Genomics Analysis Reveals the Strain-specific Probiotic Potential and Putative Antimicrobial Peptides of Bifidobacterium breve NCIM 5671.Current microbiology · 2026Article
- Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.Microbiology spectrum · 2026Article
- Phage-Microbiota Interactions in the Gut: Implications for Health and Therapeutic Strategies.Probiotics and antimicrobial proteins · 2026Review
- Restoration of the Mucosal Barrier by Lactobacillus gasseri HDS0266 and Enterococcus faecium HDS0288 in Dextran Sodium Sulfate and Clostridioides difficile-Induced Colitis Mice.Probiotics and antimicrobial proteins · 2026Article
- Genome-wide comparative and taxonomic characterization of prophages in Stenotrophomonas maltophilia.Archives of microbiology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Bacteriophages as Antibacterial Agents Against Bovine Pathobionts Associated with Foodborne Human Morbidity.Viruses · 2026Review
- Genome-resolved, preclinical safety evaluation of infant-derived Clostridium butyricum S-45-5 as a probiotic candidate.BMC microbiology · 2026Article
- A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prophages, which are an existing form of temperate phages that integrate into host genomes, have been found extensively present in diverse bacterial species. The human gut microbiome, characterized by its complexity, dynamism, and interconnectivity among multiple species, remains inadequately understood in terms of the global landscape of bacterial prophages. Here, we analyzed 43,942 human gut-derived bacterial genomes (439 species of 12 phyla) and identified 105,613 prophage regions in ~ 92% of them. 16254 complete prophages were distributed in ~ 24% of bacteria, indicating an extremely uneven prophage distribution across various species within the human gut. Among all identified prophages, ~4% possessed cross-genera (2-20 genera) integration capacity, while ~ 17% displayed broad infection host ranges (targeting 2-35 genera). Functional gene annotation revealed that antibiotic-resistance genes and toxin-related genes were detected in ~ 2.5% and ~ 5.8% of all prophages, respectively. Furthermore, through sequence alignments between our obtained prophages and publicly available human gut phageome contigs, we have observed that ~ 72% of non-redundant prophages are previously unreported genomes, and they illuminate ~ 6.5-9.5% of the individual intestinal "viral dark matter". Our study represents the first comprehensive depiction of human gut-derived prophages, provides a substantial collection of reference sequences for forthcoming human gut phageome-related investigations, and potentially enables better risk assessment of prophage dissemination.
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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.