Cited by 1,285Bacteriophages and microbial interactionsInflammatory Bowel DiseaseGut microbiota and health

The DOI matches its Crossref record; 81 of the 81 references it cites were found in a registry or an index.

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Open access

Norman, Jason M., Handley, Scott A., Baldridge, Megan T., Droit, Lindsay, Liu, Catherine Y., Keller, Brian C., Kambal, Amal, Monaco, Cynthia L., Zhao, Guoyan, Fleshner, Phillip, Stappenbeck, Thaddeus S., McGovern, Dermot P.B., Keshavarzian, Ali, Mutlu, Ece A., Sauk, Jenny, Gevers, Dirk, Xavier, Ramnik J., Wang, David, Parkes, Miles, Virgin, Herbert W.·2015·Cell

DOI 10.1016/j.cell.2015.01.002PMC PMC4312520

Open this paper in CoChat — free account Open PDF

Abstract

Decreases in the diversity of enteric bacterial populations are observed in patients with Crohn's disease (CD) and ulcerative colitis (UC). Less is known about the virome in these diseases. We show that the enteric virome is abnormal in CD and UC patients. In-depth analysis of preparations enriched for free virions in the intestine revealed that CD and UC were associated with a significant expansion of Caudovirales bacteriophages. The viromes of CD and UC patients were disease and cohort specific. Importantly, it did not appear that expansion and diversification of the enteric virome was secondary to changes in bacterial populations. These data support a model in which changes in the virome may contribute to intestinal inflammation and bacterial dysbiosis. We conclude that the virome is a candidate for contributing to, or being a biomarker for, human inflammatory bowel disease and speculate that the enteric virome may play a role in other diseases.

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

Crossref · 10.1016/j.cell.2015.01.002

Cites

81 of 81 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
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
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C., Turnbaugh, P. J., Fierer, N., & Knight, R. D. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,944
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176

Show all 81 references

Sorted by citations

Items 401–500 of 999

Etiopathogenesis of inflammatory bowel disease
de Souza, H. S. P. (2017) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000364 · Cited by 59
Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data
Bang, S., Yoo, D., Kim, S., Jhang, S. Y., Cho, S., & Kim, H. (2019) · Scientific Reports · doi:10.1038/s41598-019-46249-x · Cited by 54
Phages and Their Role in Gastrointestinal Disease: Focus on Inflammatory Bowel Disease
Marônek, M., Link, R., Ambro, Ľ., & Gardlík, R. (2020) · Cells · doi:10.3390/cells9041013 · Cited by 54
Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals
Kirsch, J. M., Brzozowski, R., Faith, D. R., Round, J. L., Secor, P. R., & Duerkop, B. A. (2021) · Annual Review of Virology · doi:10.1146/annurev-virology-091919-101238 · Cited by 55
The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis
Zheng, J., Sun, Q., Zhang, J., & Ng, S. C. (2022) · United European Gastroenterology Journal · doi:10.1002/ueg2.12338 · Cited by 57
Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy
Fan, G., Cao, F., Kuang, T., Yi, H., Zhao, C., Wang, L., Peng, J., Zhuang, Z., Xu, T., Luo, Y., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2226925 · Cited by 56
Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases
Fujiki, J., & Schnabl, B. (2023) · JHEP Reports · doi:10.1016/j.jhepr.2023.100909 · Cited by 60
Precision microbiota therapy for IBD: premise and promise
Nagayama, M., Gogokhia, L., & Longman, R. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2489067 · Cited by 58
Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants
Kim, A. H., Armah, G. E., Dennis, F. E., Wang, L., Rodgers, R., Droit, L., Baldridge, M. T., Handley, S. A., & Harris, V. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.002 · Cited by 54
Self-citation
The gut virome in inflammatory bowel diseases
Liang, G., Güemes, A. G. C., Albenberg, L. G., & Bushman, F. D. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.10.005 · Cited by 53
IgA in human health and diseases: Potential regulator of commensal microbiota
Takeuchi, T., & Ohno, H. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1024330 · Cited by 53
tRNA queuosine modification is involved in biofilm formation and virulence in bacteria
Díaz-Rullo, J., & González‐Pastor, J. E. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad667 · Cited by 57
Role of the intestinal mucosa in acute gastrointestinal GVHD
Peled, J. U., Hanash, A. M., & Jenq, R. R. (2016) · Blood · doi:10.1182/blood-2016-06-716738 · Cited by 55
Bangladeshi children with acute diarrhoea show faecal microbiomes with increased Streptococcus abundance, irrespective of diarrhoea aetiology
Kieser, S., Sarker, S. A., Sakwińska, O., Foata, F., Sultana, S., Khan, Z. A., Islam, S., Porta, N., Combremont, S., Bétrisey, B., et al. (2018) · Environmental Microbiology · doi:10.1111/1462-2920.14274 · Cited by 52
Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort
Mahnič, A., & Rupnik, M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0209209 · Cited by 57
A New Vision of IgA Nephropathy: The Missing Link
Sallustio, F., Curci, C., Leo, V. D., Gallone, A., Pesce, F., & Gesualdo, L. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010189 · Cited by 53
Machine Learning Uncovers Adverse Drug Effects on Intestinal Bacteria
McCoubrey, L. E., Elbadawi, M., Orlu, M., Gaisford, S., & Basit, A. W. (2021) · Pharmaceutics · doi:10.3390/pharmaceutics13071026 · Cited by 56
Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages
Whon, T. W., Kim, H. S., Shin, N., Sung, H., Kim, M., Kim, J. Y., Kang, W., Kim, P. S., Hyun, D., Seong, H. J., et al. (2021) · mSystems · doi:10.1128/msystems.00816-20 · Cited by 54
The gut microbiota in retinal diseases
Bringer, M.-A., Gabrielle, P., Bron, A. M., Creuzot-Garcher, C. P., & Acar, N. (2021) · Experimental Eye Research · doi:10.1016/j.exer.2021.108867 · Cited by 52
The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease
Guzzo, G. L., Andrews, J. M., & Weyrich, L. S. (2022) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izab343 · Cited by 56
Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients
Guo, R., Li, S., Zhang, Y., Zhang, Y., Wang, G., Ullah, H., Ma, Y., & Yan, Q. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00348-22 · Cited by 49
Beyond the gut bacterial microbiota: The gut virome
Columpsi, P., Sacchi, P., Zuccaro, V., Cima, S., Sarda, C., Mariani, M., Gori, A., & Bruno, R. (2016) · Journal of Medical Virology · doi:10.1002/jmv.24508 · Cited by 50
Research on the human virome: where are we and what is next
Zou, S., Caler, L., Colombini-Hatch, S., Glynn, S. A., & Srinivas, P. R. (2016) · Microbiome · doi:10.1186/s40168-016-0177-y · Cited by 51
Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions
Fariña, R., Severi, M., Carrieri, A., Miotto, E., Sabbioni, S., Trombelli, L., & Scapoli, C. (2019) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2019.05.025 · Cited by 52
Gut microbiome and multiple sclerosis: New insights and perspective
Amini, M. E., Shomali, N., Bakhshi, A., Rezaei, S., Hemmatzadeh, M., Hosseinzadeh, R., Eslami, S., Babaie, F., Aslani, S., Torkamandi, S., et al. (2020) · International Immunopharmacology · doi:10.1016/j.intimp.2020.107024 · Cited by 54
Explainable deep neural networks for novel viral genome prediction
Dasari, C. M., & Bhukya, R. (2021) · Applied Intelligence · doi:10.1007/s10489-021-02572-3 · Cited by 54
Understanding the molecular drivers of disease heterogeneity in Crohn's disease using multi-omic data integration and network analysis
Sudhakar, P., Verstockt, B., Cremer, J., Verstockt, S., Sabino, J., Ferrante, M., & Vermeire, S. (2021) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izaa281 · Cited by 49
Gut as viral reservoir: lessons from gut viromes, HIV and COVID-19
Neurath, M. F., Überla, K., & Ng, S. C. (2021) · Gut · doi:10.1136/gutjnl-2021-324622 · Cited by 50
ECCO Topical Review on Clinicopathological Spectrum and Differential Diagnosis of Inflammatory Bowel Disease
Feakins, R. M., Torres, J., Borralho, P., Burisch, J. M., Gonçalves, T. C., de Ridder, L., Driessen, A. L. C., Lobatón, T., Menchen, L. A., Mookhoek, A., et al. (2021) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjab141 · Cited by 57
Gut microbiota and inflammatory bowel disease
Chen, L., & Wang, J. (2021) · WIREs Mechanisms of Disease · doi:10.1002/wsbm.1540 · Cited by 55
Effects of bacteriophages on gut microbiome functionality
Kurilovich, E., & Geva-Zatorsky, N. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2481178 · Cited by 51
Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease
Bábíčková, J. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i40.11321 · Cited by 52
A Microbiome Foundation for the Study of Crohn’s Disease
Gevers, D., Kugathasan, S., Knights, D., Kostic, A. D., Knight, R. D., & Xavier, R. J. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.02.012 · Cited by 51
Self-citation
Phages to shape the gut microbiota?
Dahlman, S., Avellaneda-Franco, L., & Barr, J. J. (2020) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2020.09.016 · Cited by 51
Enteric Phageome Alterations in Patients With Type 2 Diabetes
Chen, Q., Ma, X., Li, C., Shen, Y., Zhu, W., Zhang, Y., Guo, X., Zhou, J., & Liu, C. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.575084 · Cited by 51
Self-citation
The dark side of the gut: Virome–host interactions in intestinal homeostasis and disease
Li, Y., Handley, S. A., & Baldridge, M. T. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20201044 · Cited by 55
Self-citation
Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD—What, Why, and How
Fiocchi, C., Dragoni, G., Iliopoulos, D., Katsanos, K. H., Hernández, V., Suzuki, K., Verstockt, B., Fiocchi, C., Torres, J., & Scharl, M. M. (2021) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjab051 · Cited by 54
Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio)
Teng, M., Li, Y., Zhao, X., White, J. C., Zhao, L., Sun, J., Zhu, W., & Wu, F. (2023) · Microbiome · doi:10.1186/s40168-023-01680-1 · Cited by 56
Temperate phages as self-replicating weapons in bacterial competition
Li, X., Lachnit, T., Fraune, S., Bosch, T. C. G., Traulsen, A., & Sieber, M. (2017) · Journal of The Royal Society Interface · doi:10.1098/rsif.2017.0563 · Cited by 48
Translating the gut microbiome: ready for the clinic?
Lynch, S. V., Ng, S. C., Shanahan, F., & Tilg, H. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0204-0 · Cited by 52
Review article: bacteriophages in gastroenterology—from biology to clinical applications
Sabino, J., Hirten, R. P., & Colombel, J. (2019) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.15557 · Cited by 53
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Mallawaarachchi, V., Roach, M. J., Decewicz, P., Papudeshi, B. N., Giles, S. K., Grigson, S. R., Bouras, G. S., Hesse, R. D., Inglis, L. K., Hutton, A. L. K., et al. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad586 · Cited by 49
Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome
Hannigan, G. D., Duhaime, M. B., Koutra, D., & Schloss, P. D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006099 · Cited by 48
Bacteriophages Contribute to Shaping Clostridioides (Clostridium) difficile Species
Fortier, L. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02033 · Cited by 52
Bacteriophages: Uncharacterized and Dynamic Regulators of the Immune System
Sinha, A., & Maurice, C. F. (2019) · Mediators of Inflammation · doi:10.1155/2019/3730519 · Cited by 51
Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome
Manrique, P., Zhu, Y., John van der, O. O. S. T., Herrema, H., Nieuwdorp, M., de Vos, W. M., & Young, M. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1897217 · Cited by 49
A universe of human gut-derived bacterial prophages: unveiling the hidden viral players in intestinal microecology
Pei, Z., Liu, Y., Chen, Y., Pan, T., Sun, X., Wang, H., Ross, R. P., Lu, W., & Chen, W. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2309684 · Cited by 48
Role of Gut Microbiota in Multiple Sclerosis and Potential Therapeutic Implications
Wang, X., Liang, Z., Wang, S., Ma, D., Zhu, M., & Feng, J. (2021) · Current Neuropharmacology · doi:10.2174/1570159x19666210629145351 · Cited by 49
Gut Microbiome as a Target of Intervention in Inflammatory Bowel Disease Pathogenesis and Therapy
Hetta, ‏. F., Ramadan, Y. N., Alharbi, A. A., Alsharif, S. M., Alkindy, T. T., Alkhamali, A., Albalawi, A. S., & El‐Amin, H. (2024) · Immuno · doi:10.3390/immuno4040026 · Cited by 54
The Microbiome in Patients With Inflammatory Diseases
Somineni, R. P., & Kugathasan, S. (2018) · Clinical Gastroenterology and Hepatology · doi:10.1016/j.cgh.2018.08.078 · Cited by 49
A theoretical model of temperate phages as mediators of gut microbiome dysbiosis
Lin, D. M., & Lin, H. C. (2019) · F1000Research · doi:10.12688/f1000research.18480.1 · Cited by 49
A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach
d’Humières, C., Touchon, M., Dion, S., Cury, J., Ghozlane, A., Garcia‐Garcerà, M., Bouchier, C., Ma, L., Denamur, É., & Rocha, E. P. C. (2019) · Scientific Reports · doi:10.1038/s41598-019-47656-w · Cited by 45
MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations
Zhu, Z., Ren, J., Michail, S. K., & Sun, F. (2019) · Genome biology · doi:10.1186/s13059-019-1773-5 · Cited by 47
The Future of Microbiome‐Based Therapeutics in Clinical Applications
Sharma, A., Das, P., Buschmann, M. M., & Gilbert, J. A. (2019) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.1677 · Cited by 50
The Role and Mechanism of Intestinal Flora in Blood Pressure Regulation and Hypertension Development
Li, J., Yang, X., Zhou, X., & Cai, J. (2020) · Antioxidants and Redox Signaling · doi:10.1089/ars.2020.8104 · Cited by 51
The gut virome of healthy children during the first year of life is diverse and dynamic
Taboada, B., Moran, P. A., Serrano-Vázquez, A., Iša, P., Rojas-Velázquez, L., Pérez-Juárez, H., López, S., Torres, J., Ximénez, C., & Arias, C. F. (2021) · PLoS ONE · doi:10.1371/journal.pone.0240958 · Cited by 44
Characterization of the gut DNA and RNA Viromes in a Cohort of Chinese Residents and Visiting Pakistanis
Yan, Q., Wang, Y., Chen, X., Jin, H., Wang, G., Guan, K., Zhang, Y., Zhang, P., Taj, A., Liang, Y., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab022 · Cited by 44
Cervicovaginal DNA Virome Alterations Are Associated with Genital Inflammation and Microbiota Composition
Kaelin, E. A., Skidmore, P. T., Łaniewski, P., Holland, L. A., Chase, D. M., Herbst‐Kralovetz, M. M., & Lim, E. S. (2022) · mSystems · doi:10.1128/msystems.00064-22 · Cited by 47
Gut Microbiome in Inflammatory Bowel Disease: Role in Pathogenesis, Dietary Modulation, and Colitis-Associated Colon Cancer
Gubatan, J. M. B., Boye, T. L., Temby, M., Sojwal, R. S., Holman, D., Sinha, S. R., Rogalla, S., & Nielsen, O. H. (2022) · Microorganisms · doi:10.3390/microorganisms10071371 · Cited by 47
The Role of Fecal Microbiota Transplantation in IBD
Fanizzi, F., D’Amico, F., Bombassaro, I., Zilli, A., Furfaro, F., Parigi, T. L., Cicerone, C., Fiorino, G., Peyrin‐Biroulet, L., Danese, S., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12091755 · Cited by 49
Mutualistic viruses and the heteronomy of life
Pradeu, T. (2016) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2016.02.007 · Cited by 51
Primary sclerosing cholangitis: 50 years of a gut–liver relationship and still no love?
Karlsen, T. H. (2016) · Gut · doi:10.1136/gutjnl-2016-312137 · Cited by 49
An expanding stage for commensal microbes in host immune regulation
Shi, Y., & Mu, L. (2017) · Cellular and Molecular Immunology · doi:10.1038/cmi.2016.64 · Cited by 46
Prediction of virus-host infectious association by supervised learning methods
Zhang, M., Yang, L., Ren, J., Ahlgren, N. A., Fuhrman, J. A., & Sun, F. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1473-7 · Cited by 47
A Previously Undescribed Highly Prevalent Phage Identified in a Danish Enteric Virome Catalog
Espen, L. V., Bak, E. G., Beller, L., Close, L., Deboutte, W., Juel, H. B., Nielsen, T., Sinar, D., Coninck, L. D., Frithioff‐Bøjsøe, C., et al. (2021) · mSystems · doi:10.1128/msystems.00382-21 · Cited by 45
Viruses in colorectal cancer
Marongiu, L., & Allgayer, H. (2021) · Molecular Oncology · doi:10.1002/1878-0261.13100 · Cited by 49
Gut Virome: Role and Distribution in Health and Gastrointestinal Diseases
Spencer, L. A., Olawuni, B., & Singh, P. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.836706 · Cited by 46
Manipulation of Gut Microbiota as a Key Target for Crohn's Disease
Rashed, R. T., Valcheva, R. S., & Dieleman, L. A. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.887044 · Cited by 52
Smoking is associated with quantifiable differences in the human lung DNA virome and metabolome
Gregory, A., Sullivan, M. B., Segal, L. N., & Keller, B. C. (2018) · Respiratory Research · doi:10.1186/s12931-018-0878-9 · Cited by 47
Self-citation
Probing the “Dark Matter” of the Human Gut Phageome: Culture Assisted Metagenomics Enables Rapid Discovery and Host-Linking for Novel Bacteriophages
Fitzgerald, C. B., Shkoporov, A. N., Upadrasta, A., Khokhlova, E. V., Ross, R. P., & Hill, C. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.616918 · Cited by 49
Understanding the Interactions Between the Ocular Surface Microbiome and the Tear Proteome
Zysset‐Burri, D. C., Schlegel, I., Lincke, J., Jaggi, D., Keller, I., Heller, M., Lagache, S. B., Wolf, S., & Zinkernagel, M. S. (2021) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.62.10.8 · Cited by 46
The impact of phage and phage resistance on microbial community dynamics
Alseth, E., Custódio, R., Sundius, S. A., Kuske, R., Brown, S. P., & Westra, E. R. (2024) · PLoS Biology · doi:10.1371/journal.pbio.3002346 · Cited by 47
Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics
Moreno, P. S., Wagner, J., Mansfield, C., Stevens, M. P., Gilkerson, J. R., & Kirkwood, C. D. (2017) · PLoS ONE · doi:10.1371/journal.pone.0178433 · Cited by 45
Biases in Viral Metagenomics-Based Detection, Cataloguing and Quantification of Bacteriophage Genomes in Human Faeces, a Review
Callanan, J., Stockdale, S. R., Shkoporov, A. N., Draper, L. A., Ross, R. P., & Hill, C. (2021) · Microorganisms · doi:10.3390/microorganisms9030524 · Cited by 43
Evaluation of the Effects of Different Bacteroides vulgatus Strains against DSS-Induced Colitis
Li, S., Wang, C., Zhang, C., Luo, Y., Cheng, Q., Yu, L., & Sun, Z. (2021) · Journal of Immunology Research · doi:10.1155/2021/9117805 · Cited by 45
Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain
Larroya, A., Pantoja, J., Codoñer‐Franch, P., & Cénit, M. C. (2021) · Frontiers in Pediatrics · doi:10.3389/fped.2021.705859 · Cited by 47
Cross-Sectional Study on the Gut Microbiome of Parkinson’s Disease Patients in Central China
Mao, L., Zhang, Y., Tian, J., Sang, M., Zhang, G., Zhou, Y., & Wang, P. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.728479 · Cited by 45
Microbial pathogenesis in inflammatory bowel diseases
Kumar, S., & Kumar, A. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105383 · Cited by 50
The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance
Jansen, D., & Matthijnssens, J. (2023) · Viruses · doi:10.3390/v15010173 · Cited by 43
Meta-omics in Inflammatory Bowel Disease Research: Applications, Challenges, and Guidelines
Valles‐Colomer, M., Darzi, Y., Vieira‐Silva, S., Falony, G., Raes, J., & Joossens, M. (2016) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjw024 · Cited by 46
A system biology perspective on environment–host–microbe interactions
Chen, L., Garmaeva, S., Zhernakova, A., Fu, J., & Wijmenga, C. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddy137 · Cited by 47
Long‐term microbiota and virome in a Zürich patient after fecal transplantation against Clostridium difficile infection
Broecker, F., Klumpp, J., & Moelling, K. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13100 · Cited by 43
Looking into Enteric Virome in Patients with IBD
Lopes, S., Andrade, P., Conde, S., Liberal, R., Dias, C. C., Fernandes, S., Pinheiro, J., Simões, J. S., Carneiro, F., Magro, F., et al. (2017) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000001167 · Cited by 43
Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion
Liu, D., Ma, Y., Jiang, X., & He, T. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3082-0 · Cited by 44
Enteric Virome and Carcinogenesis in the Gut
Emlet, C., Ruffin, M. T., & Lamendella, R. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06126-4 · Cited by 43
Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives
Raeisi, H., Noori, M., Azimirad, M., Mohebbi, S. R., Aghdaei, H. A., Yadegar, A., & Zali, M. R. (2023) · Gut Pathogens · doi:10.1186/s13099-023-00550-3 · Cited by 42
Engineering commensal bacteria to rewire host–microbiome interactions
Hwang, I. Y., & Chang, M. W. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.09.007 · Cited by 39
Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer
Zuo, W., Michail, S. K., & Sun, F. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.918010 · Cited by 44
Phages of life – the path to pharma
Forde, A., & Hill, C. (2017) · British Journal of Pharmacology · doi:10.1111/bph.14106 · Cited by 44
Gut inflammation in spondyloarthritis
Rizzo, A. G., Ferrante, A., Guggino, G., & Ciccia, F. (2017) · Best Practice & Research Clinical Rheumatology · doi:10.1016/j.berh.2018.08.012 · Cited by 41
Faecal phageome of healthy individuals: presence of antibiotic resistance genes and variations caused by ciprofloxacin treatment
Fernández‐Orth, D., Miró, E., Brown-Jaque, M., Rodríguez‐Rubio, L., Espinal, P., Rodríguez-Navarro, J., González‐López, J. J., Muniesa, M., & Navarro, F. (2018) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dky540 · Cited by 39
Th17 cells sense microbiome to promote depressive-like behaviors
Medina-Rodriguez, E. M., Watson, J., Reyes, J., Trivedi, M. H., & Beurel, E. (2023) · Microbiome · doi:10.1186/s40168-022-01428-3 · Cited by 42
Viruses and Multiple Sclerosis: From Mechanisms and Pathways to Translational Research Opportunities
Mentis, A. A., Dardiotis, E., Grigoriadis, N., Petinaki, E., & Hadjigeorgiou, G. M. (2017) · Molecular Neurobiology · doi:10.1007/s12035-017-0530-6 · Cited by 40
The Vaginal Virome—Balancing Female Genital Tract Bacteriome, Mucosal Immunity, and Sexual and Reproductive Health Outcomes?
Happel, A., Varsani, A., Balle, C., Passmore, J.-A. S., & Jaspan, H. B. (2020) · Viruses · doi:10.3390/v12080832 · Cited by 43
High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
Zünd, M., Ruscheweyh, H., Field, C. M., Meyer, N., Miguelangel Cuenca, V., Hoces, D., Hardt, W., & Sunagawa, S. (2021) · Microbiome · doi:10.1186/s40168-021-01033-w · Cited by 38
The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes
Verbanic, S., Deacon, J. M., & Chen, I. A. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02777-21 · Cited by 39
A Matching Strategy To Guide Donor Selection for Ulcerative Colitis in Fecal Microbiota Transplantation: Meta-Analysis and Analytic Hierarchy Process
Zhang, B., Yang, L., Ning, H., Cao, M., Chen, Z., Chen, Q., Lian, G., Tang, H., Wang, Q., Wang, J., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02159-21 · Cited by 41
Administration of 25,000 IU vitamin A doses at routine immunisation in young infants.
Rahman, M. M., Mahalanabis, D., Wahed, M. A., Islam, M. A., & Habte, D. (1995) · PubMed · Cited by 40
Natural mummification of the human gut preserves bacteriophage DNA
Santiago-Rodríguez, T. M., Fornaciari, G., Luciani, S., Dowd, S. E., Toranzos, G. A., Marota, I., & Cano, R. J. (2015) · FEMS Microbiology Letters · doi:10.1093/femsle/fnv219 · Cited by 39
Virome–host interactions in intestinal health and disease
Seo, S., & Kweon, M. (2019) · Current Opinion in Virology · doi:10.1016/j.coviro.2019.06.003 · Cited by 40

Authors: 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., Stappenbeck, T. S., McGovern, D. P. B., Keshavarzian, A., Mutlu, E. A., Sauk, J., Gevers, D., Xavier, R. J., Wang, D., Parkes, M., & Virgin, H. W.
Affiliations: Washington University in St. Louis (US)
Cedars-Sinai Medical Center (US)
Rush University Medical Center (US)
Harvard University (US)
Broad Institute (US)
University of Cambridge (GB)
Corresponding author: Virgin, Herbert W.
ORCID: Norman, Jason M.
Handley, Scott A.
Baldridge, Megan T.
Droit, Lindsay
Keller, Brian C.
Monaco, Cynthia L.
Zhao, Guoyan
Fleshner, Phillip
Stappenbeck, Thaddeus S.
McGovern, Dermot P.B.
Keshavarzian, Ali
Sauk, Jenny
Gevers, Dirk
Xavier, Ramnik J.
Wang, David
Parkes, Miles
Virgin, Herbert W.
Venue: Cell
Publisher: Elsevier BV
Published: 2015-01
Volume: 160
Issue: 3
Pages: 447-460
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2015.01.002
PMC: PMC4312520
OpenAlex: W2081319466
Cited by: 1,285
References: 81
Citations by year: 2026: 67 · 2025: 101 · 2024: 116 · 2023: 116 · 2022: 159 · 2021: 171 · 2020: 112 · 2019: 121 · 2018: 107 · 2017: 93 · 2016: 78 · 2015: 40
FWCI: 96.11
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 393 d)
Locations: Cell (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute for Health and Care Research
National Institutes of Health (UL1TR000448, R01OD011170)
Agency for Healthcare Research and Quality (R01HS021747, HS021747)
National Heart, Lung, and Blood Institute (T32HL007317)
National Cancer Institute (P30 CA 91842, T32CA009547, P30CA091842)
National Institute of Allergy and Infectious Diseases (AI067068, U01AI067068, R01AI084887, U54AI057160, T32AI007172, T32AI007163)
National Institute of Diabetes and Digestive and Kidney Diseases (P01DK046763, DK062413, R01DK092405, R21DK071838, DK046763-19, DK071838, U01DK062413, P30DK043351)
National Institute of Dental and Craniofacial Research (U54DE023789, U54DE023798)
National Center for Advancing Translational Sciences
National Center for Complementary and Integrative Health (AT001628, R21AT001628, R01AT007143)
Topics: Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Health Sciences › Medicine › Gastroenterology › Inflammatory Bowel Disease
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords: enteric virome, inflammatory bowel disease, Crohn's disease, ulcerative colitis, bacteriophages, Caudovirales, viral diversity, bacterial dysbiosis, intestinal inflammation, biomarkers, gut microbiota
MeSH terms: Bacteria, Colitis, Ulcerative, Crohn Disease, Feces, Humans, Cohort Studies, Case-Control Studies, Caudovirales, Microviridae, Metagenome, Dysbiosis

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

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks