The DOI matches its Crossref record; 58 of the 59 references it cites were found in a registry or an index, and 1 are not checked yet.
The human gut virome: Inter-individual variation and dynamic response to diet
Open accessAbstract
Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human "virome") in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet.
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
“Diet has also been associated with other types of microbes in the gut, such as archaea, fungi, and bacteriophage (Figure 2)45-47.”
From Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease (2014) · cites this paper as [47]
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
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
Self-citationNaive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410
Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
Brouns, S. J. J., Jore, M. M., Lundgren, M., Westra, E. R., Slijkhuis, R. J. H., Snijders, A. P. L., Dickman, M. J., Makarova, K. S., Koonin, E. V., & van der Oost, J. (2008) · Science · doi:10.1126/science.1159689 · Cited by 2,460
Suttle, C. A. (2005) · Nature · doi:10.1038/nature04160 · Cited by 2,186
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
Grissa, I., Vergnaud, G., & Pourcel, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm360 · Cited by 1,877
Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin
Waldor, M. K., & Mekalanos, J. J. (1996) · Science · doi:10.1126/science.272.5270.1910 · Cited by 1,851
Flagged first, then by citations
Research works printed but not linked: 1
- Sambrook J , Russell DW . 2001. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
Cited by
Sorted by citations
Items 501–600 of 921
The human microbiota associated with overall health
Xu, X., Wang, Z., & Zhang, X. (2013) · Critical Reviews in Biotechnology · doi:10.3109/07388551.2013.819485 · Cited by 25
Invasions of Host-Associated Microbiome Networks
Murall, C. L., Abbate, J. L., Touzel, M. P., Allen‐Vercoe, E., Alizon, S., Froissart, R., & McCann, K. S. (2017) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/bs.aecr.2016.11.002 · Cited by 26
Insights into the Human Virome Using CRISPR Spacers from Microbiomes
Hidalgo-Cantabrana, C., Sanozky-Dawes, R., & Barrangou, R. (2018) · Viruses · doi:10.3390/v10090479 · Cited by 24
Identification of bacteriophages in the vagina of pregnant women: a descriptive study
da Costa, A., Moron, A. F., Forney, L. J., Linhares, I. M., Sabino, É. C., Costa, S., Mendes‐Correa, M., & Witkin, S. S. (2020) · BJOG An International Journal of Obstetrics & Gynaecology · doi:10.1111/1471-0528.16528 · Cited by 24
Zolfo, M., Silverj, A., Blanco‐Míguez, A., Manghi, P., Rota‐Stabelli, O., Heidrich, V., Jensen, J., Maharjan, S., Franzosa, E. A., Menni, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.19.580813 · Cited by 24
Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms
Ganguly, C., Rostami, S., Long, K., Aribam, S. D., & Rajan, R. (2024) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2024.107295 · Cited by 24
Gut virome and its implications in the pathogenesis and therapeutics of inflammatory bowel disease
Wu, Y., Cheng, R., Lin, H., Li, L., Jia, Y., Philips, A., Zuo, T., & Zhang, H. (2025) · BMC Medicine · doi:10.1186/s12916-025-04016-y · Cited by 25
Microbial ecology in Hydra: Why viruses matter
Bosch, T. C. G., Grasis, J. A., & Lachnit, T. (2015) · The Journal of Microbiology · doi:10.1007/s12275-015-4695-2 · Cited by 23
Defined gut microbial communities: promising tools to understand and combat disease
Bayer, G., Ganobis, C. M., Allen‐Vercoe, E., & Philpott, D. J. (2021) · Microbes and Infection · doi:10.1016/j.micinf.2021.104816 · Cited by 27
Liu, Q., Zuo, T., Lu, W., Yeoh, Y. K., Su, Q., Xu, Z., Tang, W., Yang, K., Zhang, F., Lau, L. H. S., et al. (2022) · mSystems · doi:10.1128/msystems.01510-21 · Cited by 24
Novel Strategies for Applied Metagenomics
Moore-Connors, J., Dunn, K. A., Bielawski, J. P., & Limbergen, J. V. (2016) · Inflammatory Bowel Diseases · doi:10.1097/mib.0000000000000717 · Cited by 24
Extensive Mobilome-Driven Genome Diversification in Mouse Gut-AssociatedBacteroides vulgatusmpk
Lange, A., Beier, S., Steimle, A., Autenrieth, I. B., Huson, D. H., & Frick, J.-S. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw070 · Cited by 23
Li, J., Markowitz, R. H. G., Brooks, A., Mallott, E. K., Leigh, B. A., Olszewski, T., Zare, H., Bagheri, M., Smith, H., Friese, K. A., et al. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001758 · Cited by 24
The human phageome: niche-specific distribution of bacteriophages and their clinical implications
Rybicka, I., & Kaźmierczak, Z. M. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.01788-24 · Cited by 22
The microbiome in pediatric oncology
Rotz, S. J., & Dandoy, C. E. (2020) · Cancer · doi:10.1002/cncr.33030 · Cited by 22
Gut microbiome associated dysbiosis: Limited regimens and expanding horizons of phage therapy
Singha, B., Rawat, B. S., Venkataraman, R., Nair, T., Rosenn, E. H., & Soni, V. (2023) · Aspects of Molecular Medicine · doi:10.1016/j.amolm.2023.100029 · Cited by 23
VirNet: Deep attention model for viral reads identification
Abdelkareem, A. O., Khalil, M. I., ElAraby, M., Abbas, H. M., & Elbehery, A. H. A. (2018) · International Conference on Computer Engineering & Systems (ICCES) · doi:10.1109/icces.2018.8639400 · Cited by 23
Profiling of Human Gut Virome with Oxford Nanopore Technology
Cao, J., Zhang, Y., Dai, M., Xu, J., Chen, L., Zhang, F., Zhao, N., & Wang, J. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100012 · Cited by 22
Immunological and safety profile of bacteriophage therapy: A pre-clinical study
Gangwar, M., Rastogi, S., Singh, D., Shukla, A., Dhameja, N., Kumar, D., Kumar, R., & Nath, G. (2022) · Journal of Applied Microbiology · doi:10.1111/jam.15642 · Cited by 22
Mimicking prophage induction in the body: induction in the lab with pH gradients
Miller-Ensminger, T., Garretto, A., Stark, N., & Putonti, C. (2020) · PeerJ · doi:10.7717/peerj.9718 · Cited by 21
Sato, Y., Takebe, H., Tominaga, K., Yasuda, J., Kumagai, H., Hirooka, H., & Yoshida, T. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.01581-23 · Cited by 23
Structure and Assembly of TP901-1 Virion Unveiled by Mutagenesis
Stockdale, S. R., Collins, B., Spinelli, S., Douillard, F. P., Mahony, J., Cambillau, C., & van Sinderen, D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0131676 · Cited by 21
Linsuwanon, P., Poovorawan, Y., Li, L., Deng, X., Vongpunsawad, S., & Delwart, E. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135573 · Cited by 21
Gnotobiotic mouse model’s contribution to understanding host–pathogen interactions
Kubelková, K., Benuchova, M., Kozáková, H., Šinkora, M., Kročová, Z., Pejchal, J., & Macela, A. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2341-8 · Cited by 22
Gut virome: New key players in the pathogenesis of inflammatory bowel disease
Hetta, . F., Ahmed, R. F., Ramadan, Y. N., Fathy, H., Khorshid, M., Mabrouk, M. M., & Hashem, M. (2024) · World Journal of Methodology · doi:10.5662/wjm.v15.i2.92592 · Cited by 21
Progress and prospects of the healthy human gut virome
Stockdale, S. R., & Hill, C. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.10.001 · Cited by 21
Dennehy, J. J., & Abedon, S. T. (2021) · Springer eBooks · doi:10.1007/978-3-319-41986-2_8 · Cited by 20
Lawrence, D., Campbell, D. E., Schriefer, L. A., Rodgers, R., Walker, F. C., Turkin, M., Droit, L., Parkes, M., Handley, S. A., & Baldridge, M. T. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2029673 · Cited by 20
Implications of oral streptococcal bacteriophages in autism spectrum disorder
Zhan, T., Zhou, X., Chu, Y., Zhang, T., Zhang, J., Zhao, X., Wang, Z., Ding, R., Meng, Q., Yu, J., et al. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00355-3 · Cited by 20
Forces at play: exploring factors affecting the cancer metastasis
Riaz, F., Zhang, J., & Pan, F. (2024) · Frontiers in Immunology · doi:10.3389/fimmu.2024.1274474 · Cited by 23
Metabolites: a converging node of host and microbe to explain meta-organism
Chakraborty, N. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1337368 · Cited by 21
Chen, J., Li, J., Yiu, J. H. C., Lam, J. K. W., Wong, C., Dorweiler, B., Xu, A., & Woo, C. W. (2017) · Science Signaling · doi:10.1126/scisignal.aal3336 · Cited by 20
Self-citationFecal Microbiota Transplantation for Ulcerative Colitis: An Evolving Therapy
Sood, A., Singh, A., Midha, V., Mahajan, R., Kao, D. H., Rubin, D. T., & Bernstein, C. N. (2020) · Crohn s & Colitis 360 · doi:10.1093/crocol/otaa067 · Cited by 21
The application of the skin virome for human identification
Graham, E. H., Clarke, J., Fernando, S. C., Herr, J. R., & Adamowicz, M. S. (2022) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2022.102662 · Cited by 20
Gokulan, K., Bekele, A. Z., Drake, K. L., & Khare, S. (2018) · International Journal of Nanomedicine · doi:10.2147/ijn.s161379 · Cited by 20
Castells‐Nobau, A., Puig, I., Motger‐Albertí, A., de la Vega-Correa, L., Rosell-Díaz, M., Arnoriaga‐Rodríguez, M., Escrichs, A., Garre‐Olmo, J., Puig, J., Ramos, R., et al. (2024) · Nature Metabolism · doi:10.1038/s42255-024-01157-x · Cited by 19
Gut phages and their interactions with bacterial and mammalian hosts
Godsil, M., Ritz, N. L., Venkatesh, S., & Meeske, A. J. (2025) · Journal of Bacteriology · doi:10.1128/jb.00428-24 · Cited by 22
Asaba, C. N., Hameed, S. A., Agyei, E. K., Jacob, J. C., Oyebanji, V. O., & Ekabe, C. J. (2022) · Journal of Immunology Research · doi:10.1155/2022/7883945 · Cited by 20
Kosmopoulos, J. C., Campbell, D. E., Whitaker, R. J., & Wilbanks, E. G. (2023) · Applied and Environmental Microbiology · doi:10.1128/aem.00177-23 · Cited by 19
Zhai, X., Castro-Mejía, J. L., Gobbi, A., Aslampaloglou, A., Kot, W., Nielsen, D. S., & Deng, L. (2023) · Microbiome · doi:10.1186/s40168-023-01632-9 · Cited by 20
Diet, Gut Enterotypes and Health: Is There a Link?
Bushman, F. D., Lewis, J. D., & Wu, G. D. (2013) · Nestlé Nutrition Institute Workshop series · doi:10.1159/000351385 · Cited by 19
Self-citationConservation of streptococcal CRISPRs on human skin and saliva
Robles‐Sikisaka, R., Naidu, M., Ly, M., Salzman, J., Abeles, S. R., Boehm, T. K., & Pride, D. T. (2014) · BMC Microbiology · doi:10.1186/1471-2180-14-146 · Cited by 19
The Viral Janus: Viruses as Aetiological Agents and Treatment Options in Colorectal Cancer
Turkington, C. J. R., Varadan, A. C., Grenier, S. F., & Grasis, J. A. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.601573 · Cited by 19
Retroviral DNA Sequences as a Means for Determining Ancient Diets
Rivera-Pérez, J. I., Cano, R. J., Narganes-Storde, Y. M., Chanlatte-Baik, L., & Toranzos, G. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144951 · Cited by 19
Phages hijack a host's defence
Villion, M., & Moineau, S. (2013) · Nature · doi:10.1038/494433a · Cited by 19
Phage and bacteria diversification through a prophage acquisition ratchetPreprint
Anthenelli, M., Jasien, E., Edwards, R. A., Bailey, B., Felts, B., Katira, P., Nulton, J., Salamon, P., Rohwer, F. L., Silveira, C. B., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.08.028340 · Cited by 19
The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses
Babenko, V. V., Millard, A. D., Kulikov, E. E., Spasskaya, N. N., Letarova, M. A., Konanov, D. N., Belalov, I. S., & Letarov, A. V. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.10.036 · Cited by 18
Dong, S., Xin, Z., He, W., Zhang, Y., Xiong, J., Wang, J., Liao, Z., Wang, L., Zhong, Q., Wei, H., et al. (2022) · Food & Function · doi:10.1039/d1fo03694g · Cited by 18
Diverse Bacteriophage Roles in an Aphid-Bacterial Defensive Mutualism
Weldon, S. R., & Oliver, K. M. (2016) · Advances in environmental microbiology · doi:10.1007/978-3-319-28068-4_7 · Cited by 18
Dynamics of the human gut phageome during antibiotic treatment
Górska, A., Peter, S., Willmann, M., Autenrieth, I. B., Schlaberg, R., & Huson, D. H. (2018) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2018.03.011 · Cited by 18
Composition and Function of the Gut Microbiome
Blaut, M. (2018) · Springer eBooks · doi:10.1007/978-3-319-90545-7_2 · Cited by 20
Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease
Bhagchandani, T., Nikita, N., Verma, A., & Tandon, R. (2023) · Current Microbiology · doi:10.1007/s00284-023-03537-0 · Cited by 17
Gao, S., Fei, H., Li, Q., Lan, L., Huang, L., & Fan, P. (2024) · Nature Communications · doi:10.1038/s41467-024-45663-8 · Cited by 17
Reddy, B., Singh, K. M., Patel, A. K., Antony, A., Panchasara, H. H., & Joshi, C. G. (2014) · Molecular Biology Reports · doi:10.1007/s11033-014-3521-y · Cited by 17
Ogilvie, L. A., Nzakizwanayo, J., Guppy, F. M., Dedi, C., Diston, D., Taylor, H. D., Ebdon, J., & Jones, B. V. (2017) · The ISME Journal · doi:10.1038/s41396-017-0015-7 · Cited by 17
Microbiome and Cardiovascular Disease
Herrema, H., Nieuwdorp, M., & Groen, A. K. (2020) · Handbook of experimental pharmacology · doi:10.1007/164_2020_356 · Cited by 17
The association between enteric viruses and necrotizing enterocolitis
Chen, C., He, Y., Xiao, S., Ai, Q., & Yu, J. (2020) · European Journal of Pediatrics · doi:10.1007/s00431-020-03746-w · Cited by 17
Mogotsi, M. T., Mwangi, P. N., Bester, P. A., Mphahlele, M. J., Seheri, M. L., O’Neill, H. G., & Nyaga, M. M. (2020) · Viruses · doi:10.3390/v12111260 · Cited by 17
The Gut Virome: A Neglected Actor in Colon Cancer Pathogenesis
Renuka, R., & Dahiya, D. K. (2017) · Future Microbiology · doi:10.2217/fmb-2017-0159 · Cited by 17
Fernández, L., Duarte, A. C., Rodrı́guez, A., & García, P. (2021) · Beneficial Microbes · doi:10.3920/bm2020.0132 · Cited by 18
Attai, H., Wilde, J., Liu, R., Chopyk, J., Garcia, A. G., Allen‐Vercoe, E., & Pride, D. T. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.01135-22 · Cited by 16
Gut phageome: challenges in research and impact on human microbiota
Yu, X., Cheng, L. T., Yi, X., Li, B., Li, X., Liu, X., Liu, Z., & Kong, X. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1379382 · Cited by 16
Pharmacometabolomics Informs Viromics toward Precision Medicine
Balasopoulou, A., Patrinos, G. P., & Κάτσιλα, Θ. (2016) · Frontiers in Pharmacology · doi:10.3389/fphar.2016.00411 · Cited by 16
Sugar and Fatty Acids Ack-celerate Prophage Induction
Chatterjee, A., & Duerkop, B. A. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.012 · Cited by 16
Phage Interaction with the Mammalian Immune System
Belleghem, J. D. V., Dąbrowska, K., Vaneechoutte, M., & Barr, J. J. (2019) · Springer eBooks · doi:10.1007/978-3-030-26736-0_4 · Cited by 16
Tong, Q., Du, X., Hu, Z., Cui, L., Bie, J., Zhang, Q., Xiao, J., Lin, Y., & Wang, H. (2019) · FEMS Microbiology Letters · doi:10.1093/femsle/fnz241 · Cited by 16
Viruses in Cancers of the Digestive System: Active Contributors or Idle Bystanders?
Marônek, M., Link, R., Monteleone, G., Gardlík, R., & Stolfi, C. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218133 · Cited by 16
Xu, Y., Jiang, J., Lin, X., Shi, W., & Cao, C. (2022) · Virus Evolution · doi:10.1093/ve/veac057 · Cited by 16
Mick, E., Stern, A., & Sorek, R. (2013) · RNA Biology · doi:10.4161/rna.23929 · Cited by 16
Backseat drivers: the hidden influence of microbial viruses on disease
Hartley, M., Ronet, C., & Fasel, N. J. (2012) · Current Opinion in Microbiology · doi:10.1016/j.mib.2012.05.011 · Cited by 16
Valero, A. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14767 · Cited by 16
Polypeptides synthesized by common bacteria in the human gut improve rodent metabolism
Fan, Y., Lyu, L., Vazquez-Uribe, R., Zhang, W., Bongers, M., Koulouktsis, A., Yang, M., Sereikaité, V., Arora, T., Stankevič, E., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02064-x · Cited by 15
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
Human virome: Implications in cancer
Tamayo‐Trujillo, R., Guevara‐Ramírez, P., Cadena-Ullauri, S., Paz‐Cruz, E., Ruiz‐Pozo, V. A., & Zambrano, A. K. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e14086 · Cited by 16
Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household
Chopyk, J., Güemes, A. G. C., Ramirez‐Sanchez, C., Attai, H., Ly, M., Jones, M. B., Liu, R., Liu, C., Yang, K., Tu, X. M., et al. (2023) · BMC Microbiology · doi:10.1186/s12866-023-02949-z · Cited by 15
Identification of hidden N4-like viruses and their interactions with hosts
Zheng, K., Liang, Y., Páez-Espino, D., 黄, 思., Zou, X., Gao, C., Jiang, Y., He, H., Guo, C., 邵, 红., et al. (2023) · mSystems · doi:10.1128/msystems.00197-23 · Cited by 15
Mechanism-guided fine-tuned microbiome potentiates anti-tumor immunity in HCC
Liu, T., Guo, Y., Liao, Y., & Liu, J. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1333864 · Cited by 16
Selected Mechanisms of Action of Bacteriophages in Bacterial Infections in Animals
Urban‐Chmiel, R., & Pyzik, E. (2025) · Viruses · doi:10.3390/v17010101 · Cited by 16
The intestinal virome in children with cystic fibrosis differs from healthy controls
Coffey, M. J., Low, I., Stelzer‐Braid, S., Wemheuer, B., Garg, M., Thomas, T., Jaffé, A., Rawlinson, W. D., & Ooi, C. Y. (2020) · PLoS ONE · doi:10.1371/journal.pone.0233557 · Cited by 15
Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application
Hopson, L. M., Singleton, S. S., David, J. A., Basuchoudhary, A., Prast‐Nielsen, S., Klein, P., Sen, S., & Mazumder, R. (2020) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2020.08.011 · 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
The Microbiome in Infectious Diseases
Mitreva, M. (2016) · Elsevier eBooks · doi:10.1016/b978-0-7020-6285-8.00008-3 · Cited by 16
Assessing Species Diversity Using Metavirome Data: Methods and Challenges
Herath, D., Jayasundara, D., Ackland, D. C., Saeed, I., Tang, S., & Halgamuge, S. K. (2017) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2017.09.001 · Cited by 15
Specific changes of enteric mycobiota and virome in inflammatory bowel disease
Chu, Y., Jiang, M. Z., Xu, B., Wang, W. J., Chen, D., Li, X. W., Zhang, Y. J., & Liang, J. (2017) · Journal of Digestive Diseases · doi:10.1111/1751-2980.12570 · Cited by 15
Fast and global detection of periodic sequence repeats in large genomic resources
Mori, H., Evans-Yamamoto, D., Ishiguro, S., Tomita, M., & Yachie, N. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky890 · Cited by 14
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Gupta, A., Kumar, S., K., V., Harish, K., Sharma, A. K., & Sharma, V. K. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00469 · Cited by 14
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
Blanco‐Picazo, P., Gómez-Gómez, C., Aguiló‐Castillo, S., Fernández‐Orth, D., Cerdà‐Cuéllar, M., Muniesa, M., & Rodríguez‐Rubio, L. (2022) · Microbial Biotechnology · doi:10.1111/1751-7915.14056 · Cited by 16
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
Gut Microorganisms and Neurological Disease Perspectives
Faruqui, N. A., Prium, D. H., Mowna, S. A., Ullah, M. A., Araf, Y., Sarkar, B., Zohora, U. S., & Rahman, M. S. (2021) · Future Neurology · doi:10.2217/fnl-2020-0026 · Cited by 15
Journal quality and visibility: Is there a way out of the scientific periphery?
Marušić, A., Sambunjak, D., & Marušić, M. (2006) · PubMed · Cited by 14
Istvan, P., Birkeland, E. E., Avershina, E., Kværner, A. S., Bemanian, V., Pardini, B., Tarallo, S., de Vos, W. M., Rognes, T., Berstad, P. M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46033-0 · Cited by 13
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
Lalli, M., Salo, T. E., Hakola, L., Knip, M., Virtanen, S. M., & Vatanen, T. (2024) · American Journal of Clinical Nutrition · doi:10.1016/j.ajcnut.2024.11.011 · Cited by 14
Coffey, M. J., McKay, I. R., Doumit, M., Chuang, S., Adams, S. E., Stelzer‐Braid, S., Waters, S. A., Kasparian, N. A., Thomas, T., Jaffé, A., et al. (2020) · BMJ Open · doi:10.1136/bmjopen-2019-033916 · 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
An overview of major metagenomic studies on human microbiomes in health and disease
Cui, H., Li, Y., & Zhang, X. (2016) · Quantitative Biology · doi:10.1007/s40484-016-0078-x · Cited by 13
Li, H., Li, H., Wang, J., Guo, L., Fan, H., Zheng, H., Yang, Z., Huang, X., Chu, M., Yang, F., et al. (2019) · Virology Journal · doi:10.1186/s12985-019-1211-z · Cited by 14
Self-citationKanangat, S., & Skaljic, I. (2021) · Human Immunology · doi:10.1016/j.humimm.2021.07.009 · Cited by 14
Metadata
- Authors
- Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S. A., Wu, G. D., Lewis, J. D., & Bushman, F. D.
- Affiliations
- University of Pennsylvania (US)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-08-31
- Volume
- 21
- Issue
- 10
- Pages
- 1616-1625
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3202279
- OpenAlex
- W2097146199
- Cited by
- 935
- References
- 58
- Citations by year
- 2026: 28 · 2025: 37 · 2024: 57 · 2023: 71 · 2022: 52 · 2021: 85 · 2020: 71 · 2019: 92 · 2018: 78 · 2017: 84 · 2016: 68 · 2015: 63 · 2014: 59 · 2013: 54 · 2012: 33
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Crohn's and Colitis Foundation of America
- Pennsylvania Department of Health
- University of Pennsylvania (UL1 RR024134)
- Crohn's and Colitis Foundation
- Georgia Clinical and Translational Science Alliance
- National Institutes of Health (DK050306)
- National Institute of Allergy and Infectious Diseases (R01AI039368, AI39368)
- National Institute of Diabetes and Digestive and Kidney Diseases (UH2DK083981, P30DK050306)
- National Center for Research Resources (UL1RR024134, S10RR024525)
- 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 › Infectious Diseases › Viral gastroenteritis research and epidemiology
- Keywords
- gut virome, bacteriophages, virus-like particles, diet, dietary intervention, interindividual variability, gut microbiota, antibiotic resistance genes, viral metagenomics, viral community dynamics
- MeSH terms
- Adolescent, Adult, Bacteria, Bacteriophages, Feces, Genes, Bacterial, Genes, Viral, Humans, Repetitive Sequences, Nucleic Acid, RNA, Ribosomal, 16S, Virion, Open Reading Frames, Sequence Analysis, DNA, Diet, Fat-Restricted, Contig Mapping, Drug Resistance, Bacterial, Gastrointestinal Tract, Metagenome, Young Adult, High-Throughput Nucleotide Sequencing, Diet, High-Fat
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