Virome

Composition#

Eukaryotic Viruses (~10%)#

• Plant-derived viruses (dietary origin)
• Human viruses (enteroviruses, adenoviruses—typically low abundance in healthy individuals)
• Endogenous retroviruses (integrated in the human genome)

Virome in Disease#

Colorectal Cancer#

The CRC fecal virome shows increased network connectivity—phage-bacteria interaction networks become more complex and interconnected.

Virome dysbiosis persists even after surgical resection, suggesting the virome changes are not simply a consequence of tumor presence but may reflect a stable ecological state.^{[1]Alterations in colorectal cancer virome and its persistence after surgerySi Xian Ho, Jia-Hao Law, Chin-Wen Png et al. · 2024Open reference 1 ↓}

Schizophrenia#

124 viral operational taxonomic units (vOTUs) are enriched in schizophrenia (primarily Siphoviridae and Flandersviridae). A virome-based classifier achieved AUC 93.2%—outperforming both bacterial and mycobiome models for disease discrimination.^{[2]Metagenome-Based Characterization of the Gut Virome in Patients with SchizophreniaRen Y, Zhang P, Yu H et al. · 2025Open reference 2 ↓[3]Tao 2025 — Alterations in Fecal Bacteriome Virome Interplay and Microbiota-Derived Dysfunction in Patients with SchizophreniaShiwan Tao, Yulu Wu, Liling Xiao et al. · 2025Open reference 3 ↓}

Necrotizing Enterocolitis#

A critical finding: virome convergence occurs ~10 days before NEC onset—phage community composition shifts dramatically before clinical disease appears. Phage-mediated killing of commensal bacteria may precipitate the Proteobacteria (Pseudomonadota) bloom that characterizes NEC.^{[8]Kaelin 2022 — Gut Virome Signatures Preceding NECKaelin EA, Rodriguez C, Hall-Moore C et al. · 2022Open reference 8 ↓}

This positions the virome as a potential upstream trigger, not downstream consequence, of dysbiosis.

Autism Spectrum Disorder#

Gut phageome alterations detected in ASD, with disease-specific viral community structures distinguishing ASD children from healthy controls.^{[9]Shahin 2023 — Metagenomics Revealed a Correlation of Gut Phageome with Autism Spectrum DisorderKhashayar Shahin, Abbas Soleimani-Delfan, Zihan He et al. · 2023Open reference 9 ↓[10]Yuan 2025 -- Comparison of Gut Viral Communities Between Autism Spectrum Disorder and Healthy ChildrenMinli Yuan, Qiuxia Wang, Yan Lu et al. · 2025Open reference 10 ↓}

PCOS#

Phage-Lactobacillus coevolution supports vaginal eubiosis in healthy women; disruption of this phage-bacteria balance is observed in PCOS.^{[11]Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndromeHuang L, Wu X, Guo S et al. · 2022Open reference 11 ↓}

Cancer Immunotherapy Response#

The gut virome predicts immunotherapy response with AUC 0.768 vs 0.664 for bacteria-only models. Responder-enriched phages target SCFA producers (Faecalibacterium prausnitzii, Roseburia); non-responder phages target Clostridium/Bacteroides fragilis.^{[12]Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancerZhuo Liu, Meihong Liu, Huixiang Chen et al. · 2026Open reference 12 ↓}

Long COVID#

Reduced phage diversity in long COVID limits natural pathobiont predation, potentially contributing to persistent Proteobacteria (Pseudomonadota) enrichment and bacterial translocation.^{[13]Lu et al. 2021 — Alterations in the Composition of Intestinal DNA Virome in Patients With COVID-19Zhen-Hua Lu, Hao-Wei Zhou, Wei-Kang Wu et al. · 2021Open reference 13 ↓}

Virome-Bacteriome-Metabolite Interactions#

The virome does not operate in isolation. In schizophrenia, tripartite analysis revealed. Phage abundance correlates with bacterial host abundance (predator-prey dynamics).

Phage-mediated bacterial lysis releases metabolites that influence host neurotransmitter pathways. Virome-bacteriome-metabolite interaction networks are fundamentally reorganized in disease.^{[3]Tao 2025 — Alterations in Fecal Bacteriome Virome Interplay and Microbiota-Derived Dysfunction in Patients with SchizophreniaShiwan Tao, Yulu Wu, Liling Xiao et al. · 2025Open reference 3 ↓}

Cross-References#

• Gut Microbiome—The virome as the overlooked component
• Proteobacteria (Pseudomonadota)—Phylum whose bloom may be triggered by phage-mediated commensal killing
• dysbiosis—Virome dysbiosis as upstream trigger
• Antimicrobial Resistance—Phage therapy as alternative to antibiotics
• Gut-Brain Axis—Phage-toxin-neurodegeneration pathway
• Probiotics—Phage-probiotic coevolution in health
• Firmicutes (Bacillota)—SCFA producers targeted by responder vs. non-responder phages