The DOI matches its Crossref record; 53 of the 53 references it cites were found in a registry or an index.
Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome
Open accessPublished version of a preprint
Abstract
Colorectal cancer is a leading cause of cancer-related death in the United States and worldwide. Its risk and severity have been linked to colonic bacterial community composition. Although human-specific viruses have been linked to other cancers and diseases, little is known about colorectal cancer virus communities. We addressed this knowledge gap by identifying differences in colonic virus communities in the stool of colorectal cancer patients and how they compared to bacterial community differences. The results suggested an indirect role for the virome in impacting colorectal cancer by modulating the associated bacterial community. These findings both support the idea of a biological role for viruses in colorectal cancer and provide a new understanding of basic colorectal cancer etiology.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“The enteric virome and mycobiome (fungal microbiome) have also been linked with CRC.72–74”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [74]
In the citing paper
“These findings indicate an interaction between the virome and bacteriome in risk of CRC.72, 74”
From Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer (2020) · cites this paper as [74]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
vegan: Community Ecology Package
Oksanen, J., Simpson, G. L., Blanchet, F. G., Kindt, R., Legendre, P., Minchin, P. R., O’Hara, R. B., Sólymos, P., Stevens, M. H. H., Szöcs, E., et al. (2001) · doi:10.32614/cran.package.vegan · Cited by 27,099
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481
UCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01043-13 · Cited by 7,246
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682
Identification of Herpesvirus-Like DNA Sequences in AIDS-Sssociated Kaposi's Sarcoma
Chang, Y., Cesarman, E., Pessin, M. S., Lee, F., Culpepper, J., Knowles, D. M., & Moore, P. S. (1994) · Science · doi:10.1126/science.7997879 · Cited by 5,608
Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma
Feng, H., Shuda, M., Chang, Y., & Moore, P. S. (2008) · Science · doi:10.1126/science.1152586 · Cited by 3,208
Binning metagenomic contigs by coverage and composition
Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014) · Nature Methods · doi:10.1038/nmeth.3103 · Cited by 2,815
Colorectal cancer statistics, 2014
Siegel, R. L., Desantis, C. E., & Jemal, A. (2014) · CA A Cancer Journal for Clinicians · doi:10.3322/caac.21220 · Cited by 2,598
Intestinal inflammation targets cancer-inducing activity of the microbiota
Arthur, J. C., Perez-Chanona, E., Mühlbauer, M., Tomkovich, S., Uronis, J. M., Fan, T.-J., Campbell, B. J., Abujamel, T., Dogan, B., Rogers, A. B., et al. (2012) · Science · doi:10.1126/science.1224820 · Cited by 2,263
Li, D., Luo, R., Liu, C.-M., Leung, C.-M., Ting, H., Sadakane, K., Yamashita, H., & Lam, T. (2016) · Methods · doi:10.1016/j.ymeth.2016.02.020 · Cited by 2,106
caret: Classification and Regression Training
Kühn, M. (2007) · doi:10.32614/cran.package.caret · Cited by 1,964
Molecular Genetics of Colorectal Cancer
Fearon, E. R. (2011) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathol-011110-130235 · Cited by 1,805
Levin, B., Lieberman, D. A., McFarland, B., Smith, R. A., Brooks, D. D., Andrews, K. S., Dash, C., Giardiello, F. M., Glick, S. N., Levin, T. R., et al. (2008) · CA A Cancer Journal for Clinicians · doi:10.3322/ca.2007.0018 · Cited by 1,800
Garrett, W. S. (2015) · Science · doi:10.1126/science.aaa4972 · Cited by 1,404
Potential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375
Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease
Norman, J. M., Handley, S. A., Baldridge, M. T., Droit, L., Liu, C. Y., Keller, B. C., Kambal, A., Monaco, C. L., Zhao, G., Fleshner, P., et al. (2015) · Cell · doi:10.1016/j.cell.2015.01.002 · Cited by 1,285
Viruses in the faecal microbiota of monozygotic twins and their mothers
Reyes, A., Haynes, M. R., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F. L., & Gordon, J. I. (2010) · Nature · doi:10.1038/nature09199 · Cited by 1,230
The human gut virome: inter-individual variation and dynamic response to diet
Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2011) · Genome Research · doi:10.1101/gr.122705.111 · Cited by 935
Plankton networks driving carbon export in the oligotrophic ocean
Guidi, L., Chaffron, S., Bittner, L., Eveillard, D., Larhlimi, A., Roux, S., Darzi, Y., Audic, S., Berline, L., Brum, J. R., et al. (2016) · Nature · doi:10.1038/nature16942 · Cited by 919
Patterns and ecological drivers of ocean viral communities
Brum, J. R., Ignacio‐Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., et al. (2015) · Science · doi:10.1126/science.1261498 · Cited by 797
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
Schmieder, R., & Edwards, R. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017288 · Cited by 765
A review of clinical trials of human papillomavirus prophylactic vaccines
Schiller, J. T., Castellsagué, X., & Garland, S. M. (2012) · Vaccine · doi:10.1016/j.vaccine.2012.04.108 · Cited by 747
Microbiota organization is a distinct feature of proximal colorectal cancers
Dejea, C. M., Wick, E. C., Hechenbleikner, E. M., White, J. R., Mark Welch, J. L., Rossetti, B. J., Peterson, S. N., Snesrud, E. C., Borisy, G. G., Lazarev, M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1406199111 · Cited by 700
Explaining Microbial Population Genomics through Phage Predation
Rodriguez-Valera, F., Martin-Cuadrado, A.-B., Rodriguez-Brito, B., Pašić, L., Thingstad, T. F., Rohwer, F., & Mira, A. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2235 · Cited by 663
Origins of Highly Mosaic Mycobacteriophage Genomes
Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T., Wadsworth, C., Lewis, J. A., Jacobs-Sera, D., Falbo, J., Gross, J., Pannunzio, N. R., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00233-2 · Cited by 654
Laboratory procedures to generate viral metagenomes
Thurber, R. L. V., Haynes, M. R., Breitbart, M., Wegley, L., & Rohwer, F. L. (2009) · Nature Protocols · doi:10.1038/nprot.2009.10 · Cited by 600
The human gut microbiome as a screening tool for colorectal cancer
Zackular, J. P., Rogers, M. A. M., Ruffin, M. T., & Schloss, P. D. (2014) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-14-0129 · Cited by 551
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
Modi, S. R., Lee, H. H., Spina, C. S., & Collins, J. J. (2013) · Nature · doi:10.1038/nature12212 · Cited by 542
Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D., & Rohwer, F. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007370 · Cited by 441 · cited 1×
“have already been identified in various diseases, including periodontal disease (12), HIV (13), cystic fibrosis (14), disease resulting from antibiotic exposure (15, 16), urinary tract infections (17), and inflammatory bowel disease (18).”
BackgroundMonaco, C. L., Gootenberg, D. B., Zhao, G., Handley, S. A., Ghebremichael, M. S., Lim, E. S., Lankowski, A. J., Baldridge, M. T., Wilen, C. B., Flagg, M., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.02.011 · Cited by 414
Shuda, M., Kwun, H. J., Feng, H., Chang, Y., & Moore, P. S. (2011) · Journal of Clinical Investigation · doi:10.1172/jci46323 · Cited by 390
Baxter, N. T., Ruffin, M. T., Rogers, M. A. M., & Schloss, P. D. (2016) · Genome Medicine · doi:10.1186/s13073-016-0290-3 · Cited by 354
Hannigan, G. D., Meisel, J. S., Tyldsley, A. S., Zheng, Q., Hodkinson, B. P., SanMiguel, A. J., Minot, S. S., Bushman, F. D., & Grice, E. A. (2015) · mBio · doi:10.1128/mbio.01578-15 · Cited by 319
Baxter, N. T., Zackular, J. P., Chen, G. Y., & Schloss, P. D. (2014) · Microbiome · doi:10.1186/2049-2618-2-20 · Cited by 299
Self-citationZauber, A. G. (2015) · Digestive Diseases and Sciences · doi:10.1007/s10620-015-3600-5 · Cited by 294
Phage as a Modulator of Immune Responses
Górski, A., Międzybrodzki, R., Borysowski, J., Dąbrowska, K., Wierzbicki, P., Kniotek, M., Korczak-Kowalska, G., Olszowska-Zaremba, N., Łusiak-Szelachowska, M., Kłak, M., et al. (2012) · Advances in virus research · doi:10.1016/b978-0-12-394438-2.00002-5 · Cited by 268
Experimental coevolution of species interactions
Brockhurst, M. A., & Koskella, B. L. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.02.009 · Cited by 241
Kleiner, M., Hooper, L. V., & Duerkop, B. A. (2015) · BMC Genomics · doi:10.1186/s12864-014-1207-4 · Cited by 206
Altered Oral Viral Ecology in Association with Periodontal Disease
Ly, M., Abeles, S. R., Boehm, T. K., Robles‐Sikisaka, R., Naidu, M., Santiago-Rodríguez, T. M., & Pride, D. T. (2014) · mBio · doi:10.1128/mbio.01133-14 · Cited by 180
The human urine virome in association with urinary tract infections
Santiago-Rodríguez, T. M., Ly, M., Bonilla, N., & Pride, D. T. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00014 · Cited by 169
Coevolution can reverse predator–prey cycles
Cortez, M. H., & Weitz, J. S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317693111 · Cited by 157
Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer
Flynn, K. J., Baxter, N. T., & Schloss, P. D. (2016) · mSphere · doi:10.1128/msphere.00102-16 · Cited by 156
Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis
Zackular, J. P., Baxter, N. T., Chen, G., & Schloss, P. D. (2015) · mSphere · doi:10.1128/msphere.00001-15 · Cited by 125
Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes
Abeles, S. R., Ly, M., Santiago-Rodríguez, T. M., & Pride, D. T. (2015) · PLoS ONE · doi:10.1371/journal.pone.0134941 · Cited by 111
Impact of Phages on Two-Species Bacterial Communities
Harcombe, W. R., & Bull, J. J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.9.5254-5259.2005 · Cited by 99
Rossmann, F. S., Racek, T., Wobser, D., Puchałka, J., Rabener, E. M., Reiger, M., Hendrickx, A. P. A., Diederich, A.-K., Jung, K., Klein, C., et al. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004653 · Cited by 95
Hannigan, G. D., Duhaime, M. B., Koutra, D., & Schloss, P. D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006099 · Cited by 48
Evolutionary and functional implications of hypervariable loci within the skin virome
Hannigan, G. D., Zheng, Q., Meisel, J. S., Minot, S. S., Bushman, F. D., & Grice, E. A. (2017) · PeerJ · doi:10.7717/peerj.2959 · Cited by 28
Bacteriophages as Pathogens and Immune Modulators?
Lengeling, A., Mahajan, A., & Gally, D. L. (2013) · mBio · doi:10.1128/mbio.00868-13 · Cited by 24
Flagged first, then by citations
Cited by
Sorted by citations
Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0406-6 · Cited by 1,373
Gut microbiota in colorectal cancer: mechanisms of action and clinical applications
Wong, S. H., & Yu, J. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0209-8 · Cited by 1,392
Thomas, A. M., Manghi, P., Asnicar, F., Pasolli, E., Armanini, F., Zolfo, M., Beghini, F., Manara, S., Karcher, N., Pozzi, C., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0405-7 · Cited by 1,030
Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer
Song, M., Chan, A. T., & Sun, J. (2020) · Gastroenterology · doi:10.1053/j.gastro.2019.06.048 · Cited by 752
Gut microbiota in colorectal cancer development and therapy
Wong, C. C., & Yu, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00766-x · Cited by 779
Metadata
- Authors
- Hannigan, G. D., Duhaime, M. B., Ruffin, M. T., Koumpouras, C. C., & Schloss, P. D.
- Affiliations
- University of Michigan (US)
- Pennsylvania State University (US)
- Corresponding author
- Schloss, Patrick D.
- Venue
- mBio
- Publisher
- American Society for Microbiology
- Published
- 2018-12-21
- Volume
- 9
- Issue
- 6
- ISSN
- 2150-7511 (ISSN-L)
- 2161-2129
- PMC
- PMC6247079
- OpenAlex
- W2950868848
- Cited by
- 298
- References
- 53
- Citations by year
- 2026: 32 · 2025: 40 · 2024: 34 · 2023: 45 · 2022: 48 · 2021: 52 · 2020: 18 · 2019: 25 · 2018: 1
- FWCI
- 18.05
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mBio (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- HHS | National Institutes of Health (P30DK034933, T32AI007528, 5U01CA86400)
- Topics
- Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Oncology › Viral-associated cancers and disorders
- Keywords
- colorectal cancer, virome, human viruses, colonic microbiota, gut bacterial community, cancer etiology, viral-bacterial interactions, cancer diagnosis
- MeSH terms
- Bacteria, Bacteriophages, Feces, Humans, RNA, Ribosomal, 16S, Viruses, Colorectal Neoplasms, Cohort Studies, Metagenomics, Microbiota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review