Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)
Abstract
:1. Introduction
2. Results
2.1. Study Cohort and VLP Characterisation
2.2. Quantitative and Qualitative Assessment of Enriched VLP- and WMS-Derived Viral Genomes
2.3. Cluster Analysis and Taxonomic Assignment of the HQ-vOTUs
2.4. Detection of GI Eukaryotic DNA Viruses
2.5. Macrodiversity of Intestinal Viromes
2.6. Macrodiversity of Intestinal Bacteriomes
2.7. Predicting Disease-Associated Bacterial Hosts for the HQ-vOTUs
3. Discussion
4. Materials and Methods
4.1. Study Participants and Sample Collection
4.2. Faecal VLP and VLP DNA Isolation
4.3. Epifluorescence Microscopy (EFM)-Based Enumeration of Enriched Faecal VLPs
4.4. Transmission Electron Microscopy (TEM)
4.5. Library Preparation and Whole Metagenomic Sequencing of Enriched VLP DNA
4.6. Faecal Genomic DNA Isolation, Library Preparation and Whole Metagenomic Sequencing
4.7. Analysis of VLP and WMS HQ-vOTUs
4.7.1. Genome Assembly and Viral Mining
4.7.2. Dereplicating and Generating Non-Redundant Viral Operational Taxonomic Units (vOTUs)
4.7.3. Similarity Identification between VLP and WMS HQ-vOTU Datasets
4.7.4. Detecting Provirus and Plasmid from the VLP and WMS vOTU Datasets
4.7.5. Read Mapping, Average Coverage Calculation and Count Table Construction
4.7.6. vOTU Clustering and Taxonomic Annotation
4.7.7. Detection of Human Eukaryotic DNA Viruses
4.8. Analysis of Bacteriome
4.9. Host Predictions for VLP and WMS HQ-vOTUs
4.10. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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ME/CFS | SHHC | |
---|---|---|
Age; mean ± SD (median) | 33.8 ± 13.0 (37.0) | 53.6 ± 15.5 (58.5) |
Gender (male:female) | 0:9 | 3:5 |
Antibiotic use < 4 weeks | 0 | 0 |
Probiotic capsule supplement use < 4 weeks | 0 | 0 |
Illness duration > 6 months a | 9 | N/A b |
Self-reported with GI disorder | Four self-reported; Five non-reported | 0 |
Proviruses | Plasmids | |||
---|---|---|---|---|
All VLP-nr-vOTUs (n = 192,146) | All WMS-nr-vOTUs (n = 184,317) | All VLP-nr-vOTUs (n = 192,146) | All WMS-nr-vOTUs (n = 184,317) | |
Pre-CheckV filtration | 254 | 537 | 4119 | 5359 |
VLP-HQ-vOTUs (n = 1231) | WMS-HQ-vOTUs (n = 688) | VLP-HQ-vOTUs (n = 1231) | WMS-HQ-vOTUs (n = 688) | |
Post-CheckV filtration | 123 | 254 | 6 | 6 |
Top 20 Bacterial Genera | Hosts Shared in Both VLP and WMS | Hosts in VLP Only | Hosts in WMS Only | ||
---|---|---|---|---|---|
Alistipes | √ | ||||
Faecalibacterium | √ | ||||
Bacteroides | √ | √ d | |||
Oscillibacter a | − | − | − | ||
Bifidobacterium | √ | ||||
Ruminococcus b | √ | √ | √ | ||
Clostridium | √ | √ | |||
Parabacteroides | √ | ||||
Akkermansia | √ | ||||
Collinsella | √ | ||||
Dialister | √ | ||||
Roseburia | √ | ||||
Odoribacter | √ | ||||
Coprococcus | √ | ||||
Sutterella | √ | ||||
Eggerthella | √ | ||||
Anaerotruncus | √ | ||||
Adlercreutzia | √ | ||||
Eubacterium c | √ | √ | √ | √ |
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Hsieh, S.-Y.; Savva, G.M.; Telatin, A.; Tiwari, S.K.; Tariq, M.A.; Newberry, F.; Seton, K.A.; Booth, C.; Bansal, A.S.; Wileman, T.; et al. Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). Int. J. Mol. Sci. 2023, 24, 17267. https://doi.org/10.3390/ijms242417267
Hsieh S-Y, Savva GM, Telatin A, Tiwari SK, Tariq MA, Newberry F, Seton KA, Booth C, Bansal AS, Wileman T, et al. Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). International Journal of Molecular Sciences. 2023; 24(24):17267. https://doi.org/10.3390/ijms242417267
Chicago/Turabian StyleHsieh, Shen-Yuan, George M. Savva, Andrea Telatin, Sumeet K. Tiwari, Mohammad A. Tariq, Fiona Newberry, Katharine A. Seton, Catherine Booth, Amolak S. Bansal, Thomas Wileman, and et al. 2023. "Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus–Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)" International Journal of Molecular Sciences 24, no. 24: 17267. https://doi.org/10.3390/ijms242417267