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 accessAbstract
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.
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
“recent work suggests a role for viruses in IBD, with a significant expansion of Caudovirales bacteriophage in patients.71”
From The gut microbiota and host health: a new clinical frontier (2016) · cites this paper as [71]
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 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
Flagged first, then by citations
Cited by
Sorted by citations
Items 701–800 of 999
Comparison of PCR versus PCR-Free DNA Library Preparation for Characterising the Human Faecal Virome
Hsieh, S.-Y., Tariq, M., Telatin, A., Ansorge, R., Adriaenssens, E. M., Savva, G. M., Booth, C., Wileman, T., Hoyles, L., & Carding, S. R. (2021) · Viruses · doi:10.3390/v13102093 · Cited by 16
Esposito, A. M., Esposito, M. M., & Ptashnik, A. (2022) · Microorganisms · doi:10.3390/microorganisms10091815 · Cited by 16
Viral Safeguard: The Enteric Virome Protects against Gut Inflammation
Karst, S. M. (2016) · Immunity · doi:10.1016/j.immuni.2016.04.004 · Cited by 16
Microbiota as Therapeutic Targets
Xavier, R. J. (2016) · Digestive Diseases · doi:10.1159/000445263 · Cited by 15
Self-citationMoelling, K., & Broecker, F. (2016) · Bacteriophage · doi:10.1080/21597081.2016.1251380 · Cited by 16
Prophages in the infant gut are largely induced, and may be functionally relevant to their hostsPreprint
Redgwell, T. A., Thorsen, J., Petit, M., Deng, L., Vestergaard, G., Russel, J., Bisgaard, H. F., Nielsen, D. S., Sørensen, S. J., Stokholm, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.25.449885 · Cited by 16
Karimianghadim, R., Satokari, R. M., Yeo, S., Arkkila, P. E. T., Kao, D. H., & Pakpour, S. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1589704 · Cited by 17
Impact of Gut Microbiome on Gut Permeability in Liver and Gut Diseases
Saha, P., & Hartmann, P. (2025) · Microorganisms · doi:10.3390/microorganisms13061188 · Cited by 16
Centeno, A., Atanasova, K., Ebert, M. P., Thomann, A., & Reindl, W. (2025) · Seminars in Immunopathology · doi:10.1007/s00281-025-01066-5 · Cited by 21
Engineering bacteriophages for gut health: precision antimicrobials and beyond
Xu, M., Chen, S., Pei, H., Hu, L., & Zhang, Y. (2026) · Journal of Nanobiotechnology · doi:10.1186/s12951-026-04038-5 · Cited by 19
Garneau, J. R., Legrand, V., Marbouty, M., Press, M. O., Vik, D. R., Fortier, L., Sullivan, M. B., Bikard, D., & Monot, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-97867-3 · Cited by 15
Baaziz, H., Baker, Z. R., Franklin, H. C., & Hsu, B. B. (2022) · iScience · doi:10.1016/j.isci.2022.104146 · Cited by 18
Changes of intestinal microbiota and microbiota-based treatments in IBD
Li, Q., Zhou, S., Wang, Y., & Cong, J. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-03069-4 · Cited by 16
The gut virome in health and disease: new insights and associations
Shareefdeen, H., & Hill, C. (2022) · Current Opinion in Gastroenterology · doi:10.1097/mog.0000000000000885 · Cited by 15
Characterization of the Urinary Metagenome and Virome in Healthy Children
Wehedy, E., Murugesan, S., George, C. R., Shatat, I. F., & Khodor, S. A. (2022) · Biomedicines · doi:10.3390/biomedicines10102412 · Cited by 15
Buttimer, C., Khokhlova, E. V., Stein, L., Hueston, C. M., Govi, B., Draper, L. A., Ross, R. P., Shkoporov, A. N., & Hill, C. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2194794 · Cited by 17
Kong, L., Chen, S.-Y., Huang, S., Zheng, A.-Z., Gao, S., Ye, J., & Hua, C.-Y. (2024) · Inflammation Research · doi:10.1007/s00011-024-01854-z · Cited by 14
Boukadida, C., Peralta-Prado, A., Chávez-Torres, M., Romero-Mora, K. A., Rincón-Rubio, A., Ávila‐Ríos, S., Garrido-Rodríguez, D., Reyes‐Terán, G., & Pinto-Cardoso, S. M. (2024) · Microbiome · doi:10.1186/s40168-024-01925-7 · Cited by 15
There was collusion: Microbes in inflammatory bowel disease
Wong, S.-Y., & Cadwell, K. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007215 · Cited by 15
Defining the phenotype, pathogenesis and treatment of Crohn’s disease associated spondyloarthritis
Kumar, A., Lukin, D. J., Battat, R. J., Schwartzman, M., Mandl, L. A., Scherl, E., & Longman, R. (2020) · Journal of Gastroenterology · doi:10.1007/s00535-020-01692-w · Cited by 16
[Characteristics of gut virome and microbiome in patients with stroke].
Wang, Z., Xu, K., & Zhou, H. (2021) · PubMed Central · doi:10.12122/j.issn.1673-4254.2021.06.08 · Cited by 15
Li, Y., Zhang, F., Zheng, H., Kalasabail, S., Hicks, C., Fung, K., Preaudet, A., Putoczki, T. L., Beretov, J., Millar, E. K. A., et al. (2022) · Pathogens · doi:10.3390/pathogens11040457 · Cited by 15
An (Anti)-Inflammatory Microbiota: Defining the Role in Inflammatory Bowel Disease?
Burman, S., Hoedt, E. C., Pottenger, S., Mohd-Najman, N.-S., Cuív, P. Ó., & Morrison, M. (2016) · Digestive Diseases · doi:10.1159/000443759 · Cited by 15
Yang, H., Gan, D., Li, Y., Wang, X., Jin, L., Qin, K., Cui, C., Wu, J., & Wang, Z. (2020) · Evidence-based Complementary and Alternative Medicine · doi:10.1155/2020/5859023 · Cited by 15
New Insights into SARS-CoV-2 and Cancer Cross-Talk: Does a Novel Oncogenesis Driver Emerge?
Rapti, V., Τσαγανός, Θ., Vathiotis, I. A., Syrigos, N. K., Li, P., & Poulakou, G. (2022) · Vaccines · doi:10.3390/vaccines10101607 · Cited by 16
Mochochoko, B. M., Pohl, C. H., & O’Neill, H. G. (2022) · iScience · doi:10.1016/j.isci.2022.105870 · Cited by 14
Sciuto, M., & Catanzaro, R. (2023) · Acta Microbiologica et Immunologica Hungarica · doi:10.1556/030.2023.02134 · Cited by 15
Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis
Chen, C., Zhang, Y., Yao, X., Yan, Q., Li, S., Zhong, Q., Liu, Z., Tang, F., Liu, C., Li, H., et al. (2023) · BMC Microbiology · doi:10.1186/s12866-023-03097-0 · Cited by 14
Self-citationHu, F., Li, X., Liu, K., Li, Y., Xie, Y., Wei, C., Liu, S., Song, J., Wang, P., Shi, L., et al. (2024) · Annals of the Rheumatic Diseases · doi:10.1136/ard-2024-225564 · Cited by 14
Dysregulation of γδ intraepithelial lymphocytes precedes Crohn’s disease–like ileitis
Xu, W., Golovchenko, N. B., Martínez-Vargas, I. U., Fong, A., Rout, P., Achi, S. C., Bucar, E. B., Hsieh, J. J., Vidmar, K. J., Zhang, L., et al. (2025) · Science Immunology · doi:10.1126/sciimmunol.adk7429 · Cited by 15
Klag, T., Courth, L. F., Ostaff, M. J., Ott, G., Stange, E. F., Malek, N. P., Seifarth, W., & Wehkamp, J. (2018) · Inflammatory Intestinal Diseases · doi:10.1159/000494026 · Cited by 14
Tarris, G., de Rougemont, A., Estienney, M., Charkaoui, M., Mouillot, T., Bonnotte, B., Michiels, C., Martin, L., & Belliot, G. (2021) · mSphere · doi:10.1128/msphere.01185-20 · Cited by 14
Shi, Y., Tao, J., Li, B., Shen, X., Cheng, J., & Liu, H. (2021) · Frontiers in Veterinary Science · doi:10.3389/fvets.2021.695088 · Cited by 14
What is unknown in using microbiota as a therapeutic?
Sung, J. J. �., & Wong, S. H. (2021) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.15716 · Cited by 14
Gut Microbiota in Colorectal Cancer: Associations, Mechanisms, and Clinical Approaches
Pleguezuelos‐Manzano, C., Puschhof, J., & Clevers, H. C. (2021) · Annual Review of Cancer Biology · doi:10.1146/annurev-cancerbio-070120-095211 · Cited by 15
Li, M., Wang, C., Guo, Q., Xu, C., Xie, Z., Tan, J., Wu, S. V., Wang, P., Guo, J., Fang, Z., et al. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.846063 · Cited by 14
Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics
Stylianou, E. (2017) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-017-0298-4 · Cited by 14
Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy?
Rodríguez‐Rubio, L., Jofre, J., & Muniesa, M. (2017) · Antibiotics · doi:10.3390/antibiotics6040032 · Cited by 14
Fecal microbial transplantation
Bouri, S., & Hart, A. L. (2018) · Current Opinion in Clinical Nutrition & Metabolic Care · doi:10.1097/mco.0000000000000488 · Cited by 14
The Role of Plasmacytoid Dendritic Cells in Gut Health
Won, H.-Y., Lee, J., Ryu, D., Kim, H.-T., & Chang, S. (2019) · Immune Network · doi:10.4110/in.2019.19.e6 · Cited by 14
Metabolic phenotyping of the human microbiome
Barton, W., O’Sullivan, Ó., & Cotter, P. D. (2019) · F1000Research · doi:10.12688/f1000research.19481.1 · Cited by 14
Genome binning of viral entities from bulk metagenomics dataPreprint
Johansen, J., Plichta, D. R., Nissen, J. N., Jespersen, M. L., Shah, S. A., Deng, L., Stokholm, J., Bisgaard, H. F., Nielsen, D. S., Sørensen, S. J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.07.451412 · Cited by 14
Debray, R., Conover, A. E., & Koskella, B. L. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf065 · Cited by 13
The role of the gut and intestinal dysbiosis in the pathogenesis of spondyloarthritis
Mauro, D., Cai, B., Ciancio, A., Forte, G., Gandolfo, S., Thomas, R., Bergot, A., & Ciccia, F. (2025) · Joint Bone Spine · doi:10.1016/j.jbspin.2025.105923 · Cited by 16
HIV, AIDS, and the virome: Gut reactions
Monaco, C. L. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.010 · Cited by 13
Self-citationDistance-Based Regression Analysis for Measuring Associations
Shi, Y., Zhang, W., Liu, A., & Li, Q. (2023) · Journal of Systems Science and Complexity · doi:10.1007/s11424-023-2070-7 · Cited by 13
The Effects of Viruses on Insulin Sensitivity and Blood–Brain Barrier Function
Raber, J., Rhea, E. M., & Banks, W. A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032377 · Cited by 14
Opportunities and challenges in phage therapy for cardiometabolic diseases
Wortelboer, K., & Herrema, H. (2024) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2024.03.007 · Cited by 13
Another piece of puzzle for the human microbiome: the gut virome under dietary modulation
Zhao, F., & Wang, J. (2024) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2024.04.013 · Cited by 13
Research progress of ferroptosis and inflammatory bowel disease
Ma, B., Hu, X., Ai, X., & Zhang, Y. (2024) · BioMetals · doi:10.1007/s10534-024-00604-2 · Cited by 14
Redgwell, T. A., Thorsen, J., Petit, M., Deng, L., Vestergaard, G., Russel, J., Chawes, B., Bønnelykke, K., Bisgaard, H. F., Nielsen, D. S., et al. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00674-1 · Cited by 13
Barraza-Ortega, E., Gómez‐Gil, B., García-Gasca, T., Lizárraga, D., Díaz, N., & García-Gasca, A. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26178574 · Cited by 18
Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients
Anani, H., Destras, G., Bulteau, S., Castain, L., Semanas, Q., Burfin, G., Petrier, M., Martin, F. P., Poulain, C., Dickson, R. P., et al. (2025) · Cell Reports Medicine · doi:10.1016/j.xcrm.2025.102289 · Cited by 13
Gabashvili, E., Kobakhidze, S., Koulouris, S., Robinson, T. P., & Kotetishvili, M. (2021) · Food and Environmental Virology · doi:10.1007/s12560-021-09460-6 · Cited by 13
Kullberg, R. F. J., Hugenholtz, F., Brands, X., Kinsella, C. M., Sengers, H. P., Butler, J. M., Deijs, M., Klein, M., Faber, D. R., Scicluna, B. P., et al. (2021) · EClinicalMedicine · doi:10.1016/j.eclinm.2021.101074 · Cited by 12
Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease
Boix-Amorós, A., Monaco, H., Sambataro, E., & Clemente, J. C. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2107866 · Cited by 13
Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma
Ma, T., Ru, J., Xue, J., Schulz, S., Mirzaei, M. K., Janssen, K., Quante, M., & Deng, L. (2021) · Microorganisms · doi:10.3390/microorganisms9081701 · Cited by 13
Filamentous bacteriophage M13 induces proinflammatory responses in intestinal epithelial cells
Varadan, A. C., & Grasis, J. A. (2025) · Infection and Immunity · doi:10.1128/iai.00618-24 · Cited by 12
Li, H., Zhang, Y., Du, S., Shen, J., Liu, X., & Jing, J. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1543702 · Cited by 13
Pei, Z., Li, X., Cui, S., Yang, B. K., Lu, W., Zhao, J., Mao, B., & Chen, W. (2023) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-023-03722-0 · Cited by 12
Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes
Wilde, J., Boyes, R., Robinson, A. V., Daisley, B. A., Botschner, A. J., Brettingham, D. J. L., Macpherson, C. V., Mallory, E., & Allen‐Vercoe, E. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.04.001 · Cited by 12
Saenz, E., Montagut, N. E., Wang, B., Stein-Thöringer, C. K., Wang, K., Weng, H., Ebert, M. P., Schneider, K. M., Li, L., & Teufel, A. (2024) · Engineering · doi:10.1016/j.eng.2024.03.019 · Cited by 13
Hou, X., Ding, H., Wang, H., Wang, J., Liu, H., Hu, H., Billington, C., Wang, R., & Zhang, L. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2524540 · Cited by 17
Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome
Sandybayev, N. T., Beloussov, V., Strochkov, V. M., Solomadin, M., Granica, J., & Yegorov, S. (2022) · Microorganisms · doi:10.3390/microorganisms10122327 · Cited by 13
Wu, D., Zhang, C., Liu, Y., Yao, J., Yang, X., Wu, S., Du, J., & Yang, X. (2023) · Journal of Microbiology Immunology and Infection · doi:10.1016/j.jmii.2023.02.005 · Cited by 14
Human gut microbiome: A primer for the clinician
Kedia, S., & Ahuja, V. (2023) · JGH Open · doi:10.1002/jgh3.12902 · Cited by 12
An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases
Aw, W., & Fukuda, S. (2015) · Diseases · doi:10.3390/diseases3040341 · Cited by 15
Uhde, A., Herder, V., Khan, M. A., Ciurkiewicz, M., Schaudien, D., Teich, R., Floess, S., Baumgärtner, W., Huehn, J., & Beineke, A. (2016) · PLoS ONE · doi:10.1371/journal.pone.0161883 · Cited by 13
Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis
Ramos, E. D. S. F., Ribeiro, G. D. O., Villanova, F., Milagres, F. A. D. P., Brustulin, R., Araújo, E. L. L., Pandey, R. P., Raj, V. S., Deng, X., Delwart, E., et al. (2021) · Viruses · doi:10.3390/v13122365 · Cited by 12
Role of the intestinal mucosa in acute gastrointestinal GVHD
Peled, J. U., Hanash, A. M., & Jenq, R. R. (2016) · Hematology · doi:10.1182/asheducation-2016.1.119 · Cited by 12
Porter, N. T., Hryckowian, A. J., Merrill, B. D., Fuentes, J. J., Gardner, J. O., Glowacki, R. W. P., Singh, S., Crawford, R., Snitkin, E. S., Sonnenburg, J. L., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/521070 · Cited by 12
Hecatomb: An End-to-End Research Platform for Viral MetagenomicsPreprint
Roach, M. J., Beecroft, S. J., Mihindukulasuriya, K. A., Wang, L., Paredes, A. M., Henry-Cocks, K., Lima, L. F. O., Dinsdale, E. A., Edwards, R. A., & Handley, S. A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.15.492003 · Cited by 12
Self-citationLi, S., Yan, Q., Zhang, Y., Guo, R., Zhang, P., Lv, Q., Chen, F., Li, Z., Meng, J., Li, J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.27.522048 · Cited by 12
Pathophysiology of colitis-associated colorectal cancer
Neufert, C. F., & Neurath, M. F. (2026) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-026-01197-6 · Cited by 13
The Role of the Microbiome in the Etiology of Inflammatory Bowel Diseases
Halper-Stromberg, A., & Dalal, S. R. (2023) · Clinics in Colon and Rectal Surgery · doi:10.1055/s-0042-1760680 · Cited by 12
Phage and phage cocktails formulations
Mani, I. (2023) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2023.04.007 · Cited by 11
Exploring the virome: An integral part of human health and disease
Gholamzad, A., Khakpour, N., Hashemi, S. M. A., Goudarzi, Y., Ahmadi, P., Gholamzad, M., Mohammadi, M., & Gholamzad, M. (2024) · Pathology - Research and Practice · doi:10.1016/j.prp.2024.155466 · Cited by 13
Scheithauer, T. P. M., Wortelboer, K., Winkelmeijer, M., Verdoes, X., Aydin, Ö., Acherman, Y. I. Z., de Brauw, M. L., Nieuwdorp, M., Rampanelli, E., de Jonge, P. A., et al. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2380747 · Cited by 11
Bacteriophages: a double-edged sword in the gastrointestinal tract
Wei, Y., & Zhou, C. (2024) · Frontiers in Microbiomes · doi:10.3389/frmbi.2024.1450523 · Cited by 13
A review of neural networks for metagenomic binning
Herazo-Álvarez, J., Mora, M., Cuadros-Orellana, S., Vilches-Ponce, K., & Hernández-García, R. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf065 · Cited by 11
Rahaman, M. M., Wangchuk, P., & Sarker, S. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107608 · Cited by 12
Iannucci, A., Colella, M., Quiroga, M., Frascatani, R., Tomassini, L., Maresca, C., Franzè, E., Laudisi, F., Sica, G. S., Marafini, I., et al. (2025) · MedComm · doi:10.1002/mco2.70212 · Cited by 11
Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection
Bao, S., Wang, H., Li, W., Ji, L., Wang, X., Shen, Q., Yang, S., Zhou, C., & Zhang, W. (2022) · Journal of Medical Virology · doi:10.1002/jmv.27946 · Cited by 10
Chen, C., Chen, S., & Wang, B. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1035944 · Cited by 11
Next-generation Sequencing of the DNA Virome from Fecal Samples
Monaco, C. L., & Kwon, D. S. (2017) · BIO-PROTOCOL · doi:10.21769/bioprotoc.2159 · Cited by 11
Self-citationRands, C. M., Brüssow, H., & Zdobnov, E. M. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14746 · Cited by 11
Hosomi, S., Nishida, Y., & Fujiwara, Y. (2021) · Microorganisms · doi:10.3390/microorganisms9091870 · Cited by 11
Li, L., Sohn, J., Genco, R. J., Wactawski‐Wende, J., Goodison, S., Diaz, P. I., & Sun, Y. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010373 · Cited by 9
Spread of Bacterial Genomes in Packaged Particles
Quirós, P., Brown-Jaque, M., & Muniesa, M. (2016) · Future Microbiology · doi:10.2217/fmb.15.145 · Cited by 11
Gut Phage Biobank: a collection of bacteriophages targeting human commensal bacteria
Xing, B., Liu, C., Chen, W., Li, Z., Jing, X., Wu, C., Liu, R., Zhang, X., Xu, X., Li, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61946-0 · Cited by 14
Self-citationThe emerging role of the gut virome in necrotizing enterocolitis
Yi, C., Chen, J., & She, X. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e30496 · Cited by 10
Phylogeny and disease associations of a widespread and ancient intestinal bacteriophage lineage
de Jonge, P. A., van den Born, B. H., Zwinderman, A. H., Nieuwdorp, M., Dutilh, B. E., & Herrema, H. (2024) · Nature Communications · doi:10.1038/s41467-024-50777-0 · Cited by 12
Liu, Q., Liu, F., He, J., Zhou, M., Hou, T., & Liu, Y. (2019) · IEEE Access · doi:10.1109/access.2019.2957833 · Cited by 10
Comparison of gut viral communities in children under 5 years old and newborns
Li, H., Wang, H., Ju, H., Lv, J., Yang, S., Zhang, W., & Lu, H. (2023) · Virology Journal · doi:10.1186/s12985-023-02013-2 · Cited by 10
Li, J., Qu, W., Hu, C., Liu, Z., & Yan, H. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1132403 · Cited by 10
The Novel Role of Phage Particles in Chronic Liver Diseases
Chen, L., Hou, X., & Chu, H. (2023) · Microorganisms · doi:10.3390/microorganisms11051181 · Cited by 10
Gut microbiota in IBD goes viral
Ray, K. (2015) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2015.26 · Cited by 10
NIKOLAEVA, I. V., Shestakova, I. V., & Харисовна, М. Г. (1993) · Бюллетень Восточно-Сибирского научного центра Сибирского отделения Российской академии медицинских наук · doi:10.29413/abs.2018-3.1.5 · Cited by 10
Liu, D., Hu, X. T., He, T., & Jiang, X. (2018) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm.2018.8621214 · Cited by 10
Considering the Other Half of the Gut Microbiome: Bacteriophages
Maurice, C. F. (2019) · mSystems · doi:10.1128/msystems.00102-19 · Cited by 10
Metadata
- 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
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-01
- Volume
- 160
- Issue
- 3
- Pages
- 447-460
- ISSN
- 0092-8674 (ISSN-L)
- 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
- 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