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.
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Diet has been associated with other gut microbes, including archaea, fungi, and bacteriophage.
“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]
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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 · see citing works
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 19,770 · see citing works
<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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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., Dickman, M. J., Makarova, K. S., Koonin, E. V., & John van der, O. O. S. T. (2008) · Science · doi:10.1126/science.1159689 · Cited by 2,593 · see citing works
Suttle, C. A. (2005) · Nature · doi:10.1038/nature04160 · Cited by 2,186 · see citing works
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 · see citing works
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 · see citing works
Ecology of prokaryotic viruses
Weinbauer, M. G. (2003) · FEMS Microbiology Reviews · doi:10.1016/j.femsre.2003.08.001 · Cited by 1,775 · see citing works
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
Brüssow, H., Canchaya, C. A., & Hardt, W. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.3.560-602.2004 · Cited by 1,717 · see citing works
ARDB--Antibiotic Resistance Genes Database
Liu, B., & Pop, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn656 · Cited by 1,252 · see citing works
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 1,198 · see citing works
Assembly algorithms for next-generation sequencing data
Miller, J. R., Koren, S., & Sutton, G. G. (2010) · Genomics · doi:10.1016/j.ygeno.2010.03.001 · Cited by 1,156 · see citing works
Grissa, I., Vergnaud, G., & Pourcel, C. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-172 · Cited by 1,004 · see citing works
Functional metagenomic profiling of nine biomes
Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., et al. (2008) · Nature · doi:10.1038/nature06810 · Cited by 980 · see citing works
Genomic islands: tools of bacterial horizontal gene transfer and evolution
Juhas, M., van der Meer, J. R., Gaillard, M., Harding, R. M., Hood, D. W., & Crook, D. W. (2009) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00136.x · Cited by 980 · see citing works
Sorek, R., Kunin, V., & Hugenholtz, P. (2007) · Nature Reviews Microbiology · doi:10.1038/nrmicro1793 · Cited by 909 · see citing works
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
Sebaihia, M., Wren, B. W., Mullany, P. P., Fairweather, N. F., Minton, N. P., Stabler, R. A., Thomson, N. R., Roberts, A. P., Cerdeño-Tárraga, A. M., Wang, H., et al. (2006) · Nature Genetics · doi:10.1038/ng1830 · Cited by 877 · see citing works
Edwards, R. A., & Rohwer, F. L. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1163 · Cited by 840 · see citing works
Metagenomic Analyses of an Uncultured Viral Community from Human Feces
Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton, J., Salamon, P., & Rohwer, F. L. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.20.6220-6223.2003 · Cited by 828 · see citing works
Holins: The Protein Clocks of Bacteriophage Infections
Wang, I., Smith, D. L., & Young, R. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.799 · Cited by 802 · see citing works
Pfam: multiple sequence alignments and HMM-profiles of protein domains
Sonnhammer, E. L. L. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.320 · Cited by 774 · see citing works
Cryptic prophages help bacteria cope with adverse environments
Wang, X., Kim, Y., Ma, Q., Hong, S. H., Pokusaeva, K., Sturino, J. M., & Wood, T. K. (2010) · Nature Communications · doi:10.1038/ncomms1146 · Cited by 677 · see citing works
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 · see citing works
O’Brien, A. D., Newland, J. W., Miller, S. F., Holmes, R. K., Smith, H. W., & Formal, S. B. (1984) · Science · doi:10.1126/science.6387911 · Cited by 617 · see citing works
The Phage Proteomic Tree: a Genome-Based Taxonomy for Phage
Rohwer, F. L., & Edwards, R. A. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.16.4529-4535.2002 · Cited by 601 · see citing works
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 · see citing works
(2008) · Springer eBooks · doi:10.1007/978-1-4020-6754-9_6709 · Cited by 575 · see citing works
Kobayashi, I. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3742 · Cited by 513 · see citing works
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 · see citing works
Viral and microbial community dynamics in four aquatic environments
Rodriguez-Brito, B., Li, L., Wegley, L., Furlan, M., Angly, F. E., Breitbart, M., Buchanan, J. T., Desnues, C., Dinsdale, E. A., Edwards, R. A., et al. (2010) · The ISME Journal · doi:10.1038/ismej.2010.1 · Cited by 430 · see citing works
High Frequency of Horizontal Gene Transfer in the Oceans
McDaniel, L. D., Young, E., Delaney, J. A., Ruhnau, F., Ritchie, K. B., & Paul, J. H. (2010) · Science · doi:10.1126/science.1192243 · Cited by 403 · see citing works
Wu, G. D., Lewis, J. D., Hoffmann, C., Chen, Y.-Y., Knight, R. D., Bittinger, K. L., Hwang, J. M., Chen, J., Berkowsky, R. W., Nessel, L. A., et al. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-206 · Cited by 389 · see citing works
Self-citationYASS: enhancing the sensitivity of DNA similarity search
Noé, L., & Kucherov, G. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki478 · Cited by 374 · see citing works
Viral diversity and dynamics in an infant gut
Breitbart, M., Haynes, M. R., Kelley, S. T., Angly, F. E., Edwards, R. A., Felts, B., Mahaffy, J. M., Mueller, J. E., Nulton, J., Rayhawk, S., et al. (2008) · Research in Microbiology · doi:10.1016/j.resmic.2008.04.006 · Cited by 356 · see citing works
Horace, F. J. (1969) · Dialnet (Universidad de la Rioja) · Cited by 331 · see citing works
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
Leplae, R., Lima‐Mendez, G., & Toussaint, A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp938 · Cited by 320 · see citing works
What Antimicrobial Resistance Has Taught Us About Horizontal Gene Transfer
Barlow, M. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-853-9_23 · Cited by 283 · see citing works
Multiple displacement amplification compromises quantitative analysis of metagenomes
Yilmaz, S., Allgaier, M., & Hugenholtz, P. (2010) · Nature Methods · doi:10.1038/nmeth1210-943 · Cited by 252 · see citing works
Phage and the Origins of Molecular Biology
Cairns, J., Stent, G. S., & Watson, J. D. (2000) · Andalas University Repository (Andalas University) · Cited by 242 · see citing works
EFFECT OF RESOURCE ENRICHMENT ON A CHEMOSTAT COMMUNITY OF BACTERIA AND BACTERIOPHAGE
Bohannan, B. J. M., & Lenski, R. E. (1997) · Ecology · doi:10.1890/0012-9658(1997)078[2303:eoreoa]2.0.co;2 · Cited by 235 · see citing works
Angly, F. E., Rodriguez-Brito, B., Bangor, D., McNairnie, P., Breitbart, M., Salamon, P., Felts, B., Nulton, J., Mahaffy, J. M., & Rohwer, F. L. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-41 · Cited by 202 · see citing works
Lateral DNA transfer : mechanisms and consequences
Bushman, F. D. (2002) · Medical Entomology and Zoology · Cited by 201 · see citing works
Self-citationDawid, S. R., Roche, A. M., & Weiser, J. N. (2006) · Infection and Immunity · doi:10.1128/iai.01775-05 · Cited by 188 · see citing works
Anaerobic ammonia oxidation in a fertilized paddy soil
Zhu, G., Wang, S., Wang, Y., Wang, C., Risgaard‐Petersen, N., Jetten, M. S. M., & Yin, C. (2011) · doi:10.1038/ismej.2011 · Cited by 184 · see citing works
VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics
Yang, J., Chen, L., Sun, L., Yu, J., & Jin, Q. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm951 · Cited by 157 · see citing works
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity
Willner, D. L., Furlan, M., Schmieder, R., Grasis, J. A., Pride, D. T., Relman, D. A., Angly, F. E., Somera, T. M., Mariella, R. P., Rohwer, F. L., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000089107 · Cited by 143 · see citing works
Hoffmann, C., Hill, D. A., Minkah, N., Kirn, T., Troy, A., Artis, D., & Bushman, F. (2009) · Infection and Immunity · doi:10.1128/iai.00493-09 · Cited by 142 · see citing works
Self-citationShiga Toxin as a Bacterial Defense against a Eukaryotic Predator, Tetrahymena thermophila
Lainhart, W., Stolfa, G., & Koudelka, G. B. (2009) · Journal of Bacteriology · doi:10.1128/jb.00508-09 · Cited by 112 · see citing works
Within-host competition determines reproductive success of temperate bacteriophages
Refardt, D. (2011) · The ISME Journal · doi:10.1038/ismej.2011.30 · Cited by 107 · see citing works
Seo, H. S., Xiong, Y. Q., Mitchell, J. P., Seepersaud, R., Bayer, A. S., & Sullam, P. M. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001047 · Cited by 63 · see citing works
VEJφ, a novel filamentous phage of Vibrio cholerae able to transduce the cholera toxin genes
Campos, J., Martínez, E., Izquierdo, Y., & Fando, R. (2009) · Microbiology · doi:10.1099/mic.0.032235-0 · Cited by 40 · see citing works
The maintenance of the P1 plasmid prophage
Sternberg, N. L., & Austin, S. J. (1981) · Plasmid · doi:10.1016/0147-619x(81)90075-5 · Cited by 34 · see citing works
Calendar, R. L. (1988) · Springer eBooks · doi:10.1007/978-1-4684-5424-6 · Cited by 31 · see citing works
Effect of Resource Enrichment on a Chemostat Community of Bacteria and Bacteriophage
Bohannan, B. J. M., & Lenski, R. E. (1997) · Ecology · doi:10.2307/2265893 · Cited by 20 · see citing works
WebGBrowse—a web server for GBrowse
Podicheti, R. C., Gollapudi, R., & Dong, Q. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp239 · Cited by 19 · see citing works
Wilson, S. J. (1901) · doi:10.5962/bhl.title.61977 · Cited by 11 · see citing works
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
The impact of the gut microbiota on human health: an integrative view
Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012) · Cell · doi:10.1016/j.cell.2012.01.035 · Cited by 3,710 · see citing works
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Lloyd-Price, J., Arze, C., Ananthakrishnan, A. N., Schirmer, M., Avila-Pacheco, J., Poon, T. W., Andrews, E., Ajami, N. J., Bonham, K. S., Brislawn, C. J., et al. (2019) · Nature · doi:10.1038/s41586-019-1237-9 · Cited by 3,143 · see citing works
An integrated catalog of reference genes in the human gut microbiome
MetaHIT Consortium, Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2942 · Cited by 2,164 · see citing works
Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950 · see citing works
You are what you eat: Diet, health and the gut microbiota
Zmora, N., Suez, J., & Elinav, E. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-018-0061-2 · Cited by 1,792 · see citing works
Gut microbiota and IBD: causation or correlation?
Ni, J., Wu, G. D., Albenberg, L., & Tomov, V. T. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.88 · Cited by 1,778 · see citing works
Self-citationGut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease
Pickard, J. M., Zeng, M. Y., Caruso, R., & Núñez, G. (2017) · Immunological Reviews · doi:10.1111/imr.12567 · Cited by 1,699 · see citing works
Kang, D.-W., Adams, J. B., Gregory, A. C., Borody, T., Chittick, L., Fasano, A., Khoruts, A., Geis, E., Maldonado, J., McDonough-Means, S., et al. (2017) · Microbiome · doi:10.1186/s40168-016-0225-7 · Cited by 1,391 · see citing works
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 · see citing works
MetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184 · see citing works
Phage therapy: An alternative to antibiotics in the age of multi-drug resistance
Lin, D. M., Koskella, B. L., & Lin, H. C. (2017) · World Journal of Gastrointestinal Pharmacology and Therapeutics · doi:10.4292/wjgpt.v8.i3.162 · Cited by 1,163 · see citing works
Phage diversity, genomics and phylogeny
Dion, M. B., Oechslin, F., & Moineau, S. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0311-5 · Cited by 960 · see citing works
Bacteriophage adhering to mucus provide a non–host-derived immunity
Barr, J. J., Auro, R., Furlan, M., Whiteson, K., Erb, M. L., Pogliano, J., Stotland, A. B., Wolkowicz, R., Cutting, A. S., Doran, K. S., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1305923110 · Cited by 942 · see citing works
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
Hoffmann, C., Dollive, S., Grunberg, S., Chen, J., Li, H., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066019 · Cited by 808 · see citing works
“Recently changes in bacteriophage communities in gut have been correlated with dietary interventions [5].”
BackgroundSelf-citationSartor, R. B., & Wu, G. D. (2017) · Gastroenterology · doi:10.1053/j.gastro.2016.10.012 · Cited by 808 · see citing works
Self-citationA highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Dutilh, B. E., Cassman, N. A., McNair, K. A., Sanchez, S. E., Silva, A. E. T., Boling, L., Barr, J. J., Speth, D. R., Seguritan, V., Aziz, R. K., et al. (2014) · Nature Communications · doi:10.1038/ncomms5498 · Cited by 798 · see citing works
Mechanisms and consequences of intestinal dysbiosis
Weiss, G. A., & Hennet, T. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2509-x · Cited by 775 · see citing works
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome
Shkoporov, A. N., & Hill, C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.017 · Cited by 760 · see citing works
The human microbiome: Our second genome
Grice, E. A., & Segre, J. A. (2012) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090711-163814 · Cited by 759 · see citing works
The gut microbiota and the brain–gut–kidney axis in hypertension and chronic kidney disease
Yang, T., Richards, E. M., Pepine, C. J., & Raizada, M. K. (2018) · Nature Reviews Nephrology · doi:10.1038/s41581-018-0018-2 · Cited by 753 · see citing works
The gut–liver axis and gut microbiota in health and liver disease
Hsu, C. L., & Schnabl, B. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00904-3 · Cited by 737 · see citing works
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific
Shkoporov, A. N., Clooney, A. G., Sutton, T. D. S., Ryan, F. J., Daly, K. M., Nolan, J. A., McDonnell, S. A., Khokhlova, E. V., Draper, L. A., Forde, A., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.09.009 · Cited by 737 · see citing works
Unravelling the structural and mechanistic basis of CRISPR–Cas systems
John van der, O. O. S. T., Westra, E. R., Jackson, R. N., & Wiedenheft, B. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3279 · Cited by 715 · see citing works
CRISPR-mediated adaptive immune systems in bacteria and archaea
Sorek, R., Lawrence, C. M., & Wiedenheft, B. (2013) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072911-172315 · Cited by 668 · see citing works
Identifying viruses from metagenomic data using deep learning
Ren, J., Song, K., Deng, C., Ahlgren, N. A., Fuhrman, J. A., Li, Y., Xie, X. S., Poplin, R. E., & Sun, F. (2020) · Quantitative Biology · doi:10.1007/s40484-019-0187-4 · Cited by 668 · see citing works
Early life dynamics of the human gut virome and bacterial microbiome in infants
Lim, E. S., Zhou, Y., Zhao, G., Bauer, I. K., Droit, L., Ndao, I. M., Warner, B. B., Tarr, P. I., Wang, D., & Holtz, L. R. (2015) · Nature Medicine · doi:10.1038/nm.3950 · Cited by 644 · see citing works
The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut
Gregory, A., Zablocki, O., Zayed, A. A., Howell, A., Bolduc, B., & Sullivan, M. B. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.003 · Cited by 635 · see citing works
VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Ren, J., Ahlgren, N. A., Lu, Y. Y., Fuhrman, J. A., & Sun, F. (2017) · Microbiome · doi:10.1186/s40168-017-0283-5 · Cited by 632 · see citing works
The human virome: assembly, composition and host interactions
Liang, G., & Bushman, F. D. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00536-5 · Cited by 629 · see citing works
Self-citationDiet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease
Albenberg, L. G., & Wu, G. D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.01.058 · Cited by 606 · see citing works
Self-citationRapid evolution of the human gut virome
Minot, S. S., Bryson, A. L., Chehoud, C., Wu, G. D., Lewis, J. D., & Bushman, F. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1300833110 · Cited by 593 · see citing works
Self-citationThe Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease
Zuo, T., & Ng, S. C. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02247 · Cited by 590 · see citing works
Microbial Ecology along the Gastrointestinal Tract
Hillman, E. T., Lu, H., Yao, T., & Nakatsu, C. H. (2017) · Microbes and Environments · doi:10.1264/jsme2.me17017 · Cited by 586 · see citing works
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580 · see citing works
Genomic approaches to studying the human microbiota
Weinstock, G. M. (2012) · Nature · doi:10.1038/nature11553 · Cited by 539 · see citing works
Manrique, P., Bolduc, B., Walk, S. T., John van der, O. O. S. T., de Vos, W. M., & Young, M. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601060113 · Cited by 538 · see citing works
An enteric virus can replace the beneficial function of commensal bacteria
Kernbauer, E., Ding, Y., & Cadwell, K. (2014) · Nature · doi:10.1038/nature13960 · Cited by 513 · see citing works
Exploring host–microbiota interactions in animal models and humansPreprint
Kostic, A. D., Howitt, M. R., & Garrett, W. S. (2013) · Genes & Development · doi:10.1101/gad.212522.112 · Cited by 491 · see citing works
Host–microbiota interactions in immune-mediated diseases
Ruff, W. E., Greiling, T. M., & Kriegel, M. A. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-020-0367-2 · Cited by 489 · see citing works
Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy
De Vlaminck, I., Khush, K. K., Strehl, C., Kohli, B., Luikart, H., Neff, N. F., Okamoto, J., Snyder, T. M., Cornfield, D. N., Nicolls, M. R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.034 · Cited by 471 · see citing works
Computational approaches to predict bacteriophage–host relationships
Edwards, R. A., McNair, K. A., Faust, K., Raes, J., & Dutilh, B. E. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv048 · Cited by 453 · see citing works
Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease
Clooney, A. G., Sutton, T., Shkoporov, A. N., Holohan, R., Daly, K. M., O’Regan, O., Ryan, F. J., Draper, L. A., Plevy, S. E., Ross, R. P., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.10.009 · Cited by 441 · see citing works
Going viral: next-generation sequencing applied to phage populations in the human gut
Reyes, A., Semenkovich, N. P., Whiteson, K., Rohwer, F. L., & Gordon, J. I. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2853 · Cited by 433 · see citing works
Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses
Enault, F., Briet, A., Bouteille, L., Roux, S., Sullivan, M. B., & Petit, M. (2016) · The ISME Journal · doi:10.1038/ismej.2016.90 · Cited by 432 · see citing works
Metagenome-wide association studies: fine-mining the microbiome
Wang, J., & Jia, H. (2016) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2016.83 · Cited by 429 · see citing works
The unexhausted potential of E. coli
Blount, Z. D. (2015) · eLife · doi:10.7554/elife.05826 · Cited by 420 · see citing works
Gut mucosal virome alterations in ulcerative colitis
Zuo, T., Lu, X., Zhang, Y., Cheung, C. P., Lam, S., Zhang, F., Tang, W., Ching, J. Y. L., Zhao, R., Chan, P. K. S., et al. (2019) · Gut · doi:10.1136/gutjnl-2018-318131 · Cited by 417 · see citing works
Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System
Van Belleghem, J. D., Dąbrowska, K., Vaneechoutte, M., Barr, J. J., & Bollyky, P. L. (2018) · Viruses · doi:10.3390/v11010010 · Cited by 408 · see citing works
Monaco, 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 405 · see citing works
Ménage à trois in the human gut: interactions between host, bacteria and phages
Mirzaei, M. K., & Maurice, C. F. (2017) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2017.30 · Cited by 404 · see citing works
Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes
Nakatsu, G., Zhou, H., Wu, W. K. K., Wong, S. H., Coker, O. O., Dai, Z., Li, X., Szeto, C.-H., Sugimura, N., Lam, T. Y.-T., et al. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.04.018 · Cited by 386 · see citing works
Periodontal Disease: The Good, The Bad, and The Unknown
Sedghi, L. M., Bacino, M. S., & Kapila, Y. L. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.766944 · Cited by 385 · see citing works
A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity
Seed, K. D., Lazinski, D. W., Calderwood, S. B., & Camilli, A. (2013) · Nature · doi:10.1038/nature11927 · Cited by 375 · see citing works
A metagenomic insight into our gut's microbiome
Lepage, P., Leclerc, M., Joossens, M., Mondot, S., Blottière, H. M., Raes, J., Ehrlich, S. D., & Dore, J. M. (2012) · Gut · doi:10.1136/gutjnl-2011-301805 · Cited by 371 · see citing works
Regulation of intestinal homeostasis and immunity with probiotic lactobacilli
van Baarlen, P., Wells, J. M., & Kleerebezem, M. (2013) · Trends in Immunology · doi:10.1016/j.it.2013.01.005 · Cited by 369 · see citing works
Bacteriophage-mediated spread of bacterial virulence genes
Penadés, J. R., Chen, J. Y.-S., Quiles‐Puchalt, N., Carpena, N., & Novick, R. P. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.019 · Cited by 368 · see citing works
Self-citationYang, Y., Li, B. J., Ju, F., & Zhang, T. (2013) · Environmental Science & Technology · doi:10.1021/es4017365 · Cited by 358 · see citing works
Gnotobiotic mouse model of phage–bacterial host dynamics in the human gut
Reyes, A., Wu, M., McNulty, N. P., Rohwer, F. L., & Gordon, J. I. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319470110 · Cited by 355 · see citing works
Host–microorganism interactions in lung diseases
Marsland, B. J., & Gollwitzer, E. S. (2014) · Nature reviews. Immunology · doi:10.1038/nri3769 · Cited by 351 · see citing works
Human Gut Microbiota: Repertoire and Variations
Lagier, J., Million, M., Hugon, P., Armougom, F., & Raoult, D. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00136 · Cited by 329 · see citing works
Duranti, S., Lugli, G. A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferretti, P., Gorfer, V., Ferrario, C., Milani, C., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0282-6 · Cited by 327 · see citing works
The gut microbiome, diet, and links to cardiometabolic and chronic disorders
Aron‐Wisnewsky, J., & Clément, K. (2015) · Nature Reviews Nephrology · doi:10.1038/nrneph.2015.191 · Cited by 327 · see citing works
CRISPR–Cas systems: beyond adaptive immunity
Westra, E. R., Buckling, A., & Fineran, P. C. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3241 · Cited by 322 · see citing works
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition
Reyes, A., Blanton, L. V., Cao, S., Zhao, G., MANARY, M. J., Trehan, I., Smith, M. I., Wang, D., Virgin, H. W., Rohwer, F. L., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1514285112 · Cited by 321 · see citing works
Cook, R., Hooton, S., Trivedi, U. H., King, L., Dodd, C. E. R., Hobman, J. L., Stekel, D. J., Jones, M. A., & Millard, A. D. (2021) · Microbiome · doi:10.1186/s40168-021-01010-3 · Cited by 318 · see citing works
Microbiome therapeutics — Advances and challenges
Mimee, M., Citorik, R. J., & Lu, T. K. (2016) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2016.04.032 · Cited by 317 · see citing works
The human gut microbiota and virome: Potential therapeutic implications
Scarpellini, E., Ianiro, G., Attili, F., Bassanelli, C., Santis, A. D., & Gasbarrini, A. (2015) · Digestive and Liver Disease · doi:10.1016/j.dld.2015.07.008 · Cited by 315 · see citing works
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 312 · see citing works
Self-citationDiagnostic potential and interactive dynamics of the colorectal cancer virome
Hannigan, G. D., Duhaime, M. B., Ruffin, M. T., Koumpouras, C. C., & Schloss, P. D. (2018) · mBio · doi:10.1128/mbio.02248-18 · Cited by 298 · see citing works
Resident viruses and their interactions with the immune system
Duerkop, B. A., & Hooper, L. V. (2013) · Nature Immunology · doi:10.1038/ni.2614 · Cited by 297 · see citing works
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
Guerin, E., Shkoporov, A. N., Stockdale, S. R., Clooney, A. G., Ryan, F. J., Sutton, T., Draper, L. A., González-Tortuero, E., Ross, R. P., & Hill, C. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.10.002 · Cited by 297 · see citing works
Blaser, M. J. (2014) · Journal of Clinical Investigation · doi:10.1172/jci78366 · Cited by 296 · see citing works
The microbiota–gut–brain axis in gastrointestinal disorders: stressed bugs, stressed brain or both?
Palma, G. D., Collins, S. M., Berčík, P., & Verdu, E. F. (2014) · The Journal of Physiology · doi:10.1113/jphysiol.2014.273995 · Cited by 293 · see citing works
An integrative view of microbiome-host interactions in inflammatory bowel diseases
Wlodarska, M., Kostic, A. D., & Xavier, R. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.04.008 · Cited by 287 · see citing works
Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children
Zhao, G., Vatanen, T., Droit, L., Park, A., Kostic, A. D., Poon, T. W., Vlamakis, H. C., Siljander, H., Härkönen, T., Hämäläinen, A.-M., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706359114 · Cited by 279 · see citing works
Enhanced virome sequencing using targeted sequence capturePreprint
Wylie, T., Wylie, K. M., Herter, B. N., & Storch, G. A. (2015) · Genome Research · doi:10.1101/gr.191049.115 · Cited by 267 · see citing works
Bikel, S., Valdez-Lara, A., Cornejo-Granados, F., Rico, K., Canizales-Quinteros, S., Soberón, X., Del Pozo-Yauner, L., & Ochoa-Leyva, A. (2015) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2015.06.001 · Cited by 263 · see citing works
Mills, S., Shanahan, F., Stanton, C., Hill, C., Coffey, A., & Ross, R. P. (2013) · Gut Microbes · doi:10.4161/gmic.22371 · Cited by 263 · see citing works
CRISPR–Cas in mobile genetic elements: counter-defence and beyond
Faure, G., Shmakov, S., Yan, W. X., Cheng, D. R., Scott, D. A., Peters, J. E., Makarova, K. S., & Koonin, E. V. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0204-7 · Cited by 262 · see citing works
Transfer of antibiotic-resistance genes via phage-related mobile elements
Brown-Jaque, M., Calero‐Cáceres, W., & Muniesa, M. (2015) · Plasmid · doi:10.1016/j.plasmid.2015.01.001 · Cited by 259 · see citing works
A virocentric perspective on the evolution of life
Koonin, E. V., & Dolja, V. V. (2013) · Current Opinion in Virology · doi:10.1016/j.coviro.2013.06.008 · Cited by 259 · see citing works
Tisza, M. J., & Buck, C. B. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023202118 · Cited by 254 · see citing works
The Human Gut Phage Community and Its Implications for Health and Disease
Manrique, P., Dills, M., & Young, M. (2017) · Viruses · doi:10.3390/v9060141 · Cited by 253 · see citing works
The microbiota in inflammatory bowel disease
Sheehan, D., Moran, C. P., & Shanahan, F. (2015) · Journal of Gastroenterology · doi:10.1007/s00535-015-1064-1 · Cited by 249 · see citing works
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Edwards, R. A., Vega, A. A., Norman, H. M., Ohaeri, M. C., Levi, K., Dinsdale, E. A., Cinek, O., Aziz, R. K., McNair, K. A., Barr, J. J., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0494-6 · Cited by 247 · see citing works
Accuracy of Next Generation Sequencing Platforms
Fox, E., & Reid-Bayliss, K. S. (2014) · Journal of Next Generation Sequencing & Applications · doi:10.4172/2469-9853.1000106 · Cited by 247 · see citing works
Viertel, T. M., Ritter, K., & Horz, H. (2014) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dku173 · Cited by 246 · see citing works
Evolutionary Ecology of Prokaryotic Immune Mechanisms
van Houte, S., Buckling, A., & Westra, E. R. (2016) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00011-16 · Cited by 243 · see citing works
Review article: the human intestinal virome in health and disease
Carding, S. R., Davis, N., & Hoyles, L. (2017) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.14280 · Cited by 243 · see citing works
Belleghem, J. D. V., Clément, F., Merabishvili, M., Lavigne, R., & Vaneechoutte, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-08336-9 · Cited by 242 · see citing works
Metavir 2: new tools for viral metagenome comparison and assembled virome analysis
Roux, S., Tournayre, J., Mahul, A., Debroas, D., & Enault, F. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-76 · Cited by 234 · see citing works
Factors determining phage stability/activity: challenges in practical phage application
Jończyk‐Matysiak, E., Łodej, N., Kula, D., Owczarek, B., Orwat, F., Międzybrodzki, R., Neuberg, J., Bagińska, N., Weber‐Dąbrowska, B., & Górski, A. (2019) · Expert Review of Anti-infective Therapy · doi:10.1080/14787210.2019.1646126 · Cited by 230 · see citing works
Oh, J., Alexander, L. M., Pan, M., Schueler, K. L., Keller, M. P., Attie, A., Walter, J., & van Pijkeren, J. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2018.11.016 · Cited by 224 · see citing works
Characterization of virus-like particles associated with the human faecal and caecal microbiota
Hoyles, L., McCartney, A. L., Neve, H., Gibson, G. R., Sanderson, J. D., Heller, K. J., & van Sinderen, D. (2014) · Research in Microbiology · doi:10.1016/j.resmic.2014.10.006 · Cited by 223 · see citing works
Metagenomic analysis of double-stranded DNA viruses in healthy adults
Wylie, K. M., Mihindukulasuriya, K. A., Zhou, Y., Sodergren, E. J., Storch, G. A., & Weinstock, G. M. (2014) · BMC Biology · doi:10.1186/s12915-014-0071-7 · Cited by 223 · see citing works
Phages and their potential to modulate the microbiome and immunity
Federici, S., Nobs, S. P., & Elinav, E. (2021) · Cellular & Molecular Immunology · doi:10.1038/s41423-020-00532-4 · Cited by 222 · see citing works
New insights into intestinal phages
Sausset, R., Petit, M., Gaboriau‐Routhiau, V., & Paepe, M. D. (2020) · Mucosal Immunology · doi:10.1038/s41385-019-0250-5 · Cited by 220 · see citing works
Antibiotics in Feed Induce Prophages in Swine Fecal Microbiomes
Allen, H. K., Looft, T. P., Bayles, D. O., Humphrey, S. B., Levine, U. Y., Alt, D. P., & Stanton, T. B. (2011) · mBio · doi:10.1128/mbio.00260-11 · Cited by 217 · see citing works
Lysogeny is prevalent and widely distributed in the murine gut microbiota
Kim, M., & Bae, J. (2018) · The ISME Journal · doi:10.1038/s41396-018-0061-9 · Cited by 217 · see citing works
When a virus is not a parasite: the beneficial effects of prophages on bacterial fitness
Bondy‐Denomy, J., & Davidson, A. R. (2014) · The Journal of Microbiology · doi:10.1007/s12275-014-4083-3 · Cited by 214 · see citing works
- 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
- Physical Sciences › Environmental Science › Ecology › 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
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