A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology
Open accessAbstract
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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97.0% of E. coli strains harbor complete prophages, and 87.0% of E. coli strains contain prophage regions.
“97.0% of E. coli strains harbor complete prophages, and 87.0% of E. coli strains contain prophage regions.”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [142]
The Results section ('The overall landscape of prophage elements harbored in human gut-derived bacteria'; page unavailable) reports complete prophages in 97.0% of E. coli strains. It does not report that 87.0% of E. coli strains contain prophage regions, so the second percentage is unsupported by our copy. (LLM, conf=0.90)
Experimental — accuracy not yet measuredSome prophages can integrate across different bacterial genera, although this is relatively rare (~4% of prophages).
“some prophages could have the ability to integrate across different bacterial genera, although this is relatively rare (~ 4% of prophages) [142].”
From Selection, Comparative Genomics, and Potential Probiotic Features of Escherichia coli 5C, a pks-Negative Strain Isolated from Healthy Infant Donor Feces (2026) · cites this paper as [142]
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Self-citationTools and approaches to study the human gut virome: from the bench to bioinformatics
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Human gut strains of Desulfovibrio piger exhibit spontaneous induction of multiple prophages
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- Authors
- Pei, Z., Liu, Y., Chen, Y., Pan, T., Sun, X., Wang, H., Ross, R. P., Lu, W., & Chen, W.
- Affiliations
- Jiangnan University (CN)
- Corresponding author
- Lu, Wenwei
- Venue
- Gut Microbes
- Publisher
- Informa UK Limited
- Published
- 2024-02
- Volume
- 16
- Issue
- 1
- Pages
- 2309684-2309684
- ISSN
- 1949-0976 (ISSN-L)
- 1949-0984
- PMC
- PMC10841027
- OpenAlex
- W4391451088
- Cited by
- 48
- References
- 62
- Citations by year
- 2026: 25 · 2025: 18 · 2024: 5
- FWCI
- 13.13
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Gut Microbes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Key Research and Development Program of China (2022YFF1100203)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- human gut microbiome, temperate phages, antibiotic resistance genes, toxin genes, viral dark matter, gut phageome
- MeSH terms
- Gastrointestinal Microbiome, Bacteria, Humans, Phylogeny, Genome, Viral, Genome, Bacterial, Prophages, Host Specificity
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