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

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

Interactions of Bacteriophages with Animal and Human Organisms—Safety Issues in the Light of Phage Therapy

Podlacha, M., Grabowski, Ł., Kosznik-Kwaśnicka, K., Zdrojewska, K., Stasiłojć, M., Węgrzyn, G., & Węgrzyn, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22168937 · Cited by 132

Enteric Virome and Bacterial Microbiota in Children With Ulcerative Colitis and Crohn Disease

Fernandes, M. A., Verstraete, S. G., Phan, T. G., Deng, X., Stekol, E., LaMere, B. J., Lynch, S. V., Heyman, M. B., & Delwart, E. (2018) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000002140 · Cited by 124

vRhyme enables binning of viral genomes from metagenomes

Kieft, K., Adams, A., Salamzade, R., Kalan, L., & Anantharaman, K. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac341 · Cited by 119

Intestinal phages interact with bacteria and are involved in human diseases

Shuwen, H., & Kefeng, D. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2113717 · Cited by 124

Human Microbiome and its Association With Health and Diseases

Thani, A. A. A., Marei, H. E. S., Hamdi, W. S., Nasrallah, G. K., Zowalaty, M. E. E., Khodor, S. A., Al‐Asmakh, M., Aziz, H. A., & Cenciarelli, C. (2015) · Journal of Cellular Physiology · doi:10.1002/jcp.25284 · Cited by 130

Bacteriophages in the gastrointestinal tract and their implications

Łusiak-Szelachowska, M., Weber‐Dąbrowska, B., Jończyk‐Matysiak, E., Wojciechowska, R., & Górski, A. (2017) · Gut Pathogens · doi:10.1186/s13099-017-0196-7 · Cited by 127

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Pratama, A. A., Bolduc, B., Zayed, A. A., Zhong, Z.-P., Guo, J., Vik, D. R., Gazitúa, M. C., Wainaina, J. M., Roux, S., & Sullivan, M. B. (2021) · PeerJ · doi:10.7717/peerj.11447 · Cited by 122

Immunogenicity of bacteriophages

Champagne-Jorgensen, K., Luong, T., Darby, T., & Roach, D. R. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.04.008 · Cited by 115

The gut microbiome as a target for IBD treatment: are we there yet

Knox, N. C., Forbes, J. D., Van Domselaar, G., & Bernstein, C. N. (2019) · Current Treatment Options in Gastroenterology · doi:10.1007/s11938-019-00221-w · Cited by 117

Transfer of Viral Communities between Human Individuals during Fecal Microbiota Transplantation

Chehoud, C., Dryga, A., Hwang, Y., Nagy‐Szakal, D., Hollister, E. B., Luna, R. A., Versalovic, J. A., Kellermayer, R., & Bushman, F. D. (2016) · mBio · doi:10.1128/mbio.00322-16 · Cited by 123

Phages in the Gut Ecosystem

Zuppi, M., Hendrickson, H. L., O'Sullivan, J. M., & Vatanen, T. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.822562 · Cited by 124

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

Hayes, S., Mahony, J., Nauta, A., & van Sinderen, D. (2017) · Viruses · doi:10.3390/v9060127 · Cited by 119

Emollient use alters skin barrier and microbes in infants at risk for developing atopic dermatitis

Glatz, M., Jo, J., Kennedy, E. A., Polley, E. C., Segre, J. A., Simpson, E. L., & Kong, H. H. (2018) · PLoS ONE · doi:10.1371/journal.pone.0192443 · Cited by 116

The Intestinal Virome and Immunity

Neil, J. A., & Cadwell, K. (2018) · The Journal of Immunology · doi:10.4049/jimmunol.1800631 · Cited by 117

The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review

López, R. L., Burgos, M. J. G., Gálvez, A., & Pulido, R. P. (2016) · Apmis · doi:10.1111/apm.12609 · Cited by 116

Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

Shkoporov, A. N., Khokhlova, E. V., Stephens, N., Hueston, C. M., Seymour, S., Hryckowian, A. J., Scholz, D., Ross, R. P., & Hill, C. (2021) · BMC Biology · doi:10.1186/s12915-021-01084-3 · Cited by 115

Genome binning of viral entities from bulk metagenomics data

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. (2022) · Nature Communications · doi:10.1038/s41467-022-28581-5 · Cited by 116

Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

Nishijima, S., Nagata, N., Kiguchi, Y., Kojima, Y., Miyoshi‐Akiyama, T., Kimura, M., Ohsugi, M., Ueki, K., Oka, S., Mizokami, M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-32832-w · Cited by 120

Alignment-Free Sequence Analysis and Applications

Ren, J., Bai, X., Lu, Y. Y., Tang, K., Wang, Y., Reinert, G., & Sun, F. (2018) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-080917-013431 · Cited by 116

Bacteriocins and bacteriophage; a narrow-minded approach to food and gut microbiology

Mills, S., Ross, R. P., & Hill, C. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux022 · Cited by 117

Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease

Sankarasubramanian, J., Ahmad, R., Avuthu, N., Singh, A. B., & Guda, C. (2020) · Frontiers in Medicine · doi:10.3389/fmed.2020.606298 · Cited by 117

Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease

Ungaro, F., Massimino, L., Furfaro, F., Rimoldi, V., Peyrin‐Biroulet, L., D’Alessio, S., & Danese, S. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1511664 · Cited by 116

Pathogenesis of Crohn's disease

Boyapati, R. K., Satsangi, J. J., & Ho, G. (2015) · F1000Prime Reports · doi:10.12703/p7-44 · Cited by 117

DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach

Wu, S., Fang, Z., Tan, J., Li, M., Wang, C., Guo, Q., Xu, C., Jiang, X., & Zhu, H. (2021) · GigaScience · doi:10.1093/gigascience/giab056 · Cited by 110

Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation

Adiliaghdam, F., Amatullah, H., Digumarthi, S., Saunders, T. L., Rahman, R., Wong, L. P., Sadreyev, R. I., Droit, L., Paquette, J., Goyette, P., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.abn6660 · Cited by 109

The interplay between intestinal bacteria and host metabolism in health and disease: lessons fromDrosophila melanogaster

Wong, A. C.-N., Vanhove, A. S., & Watnick, P. I. (2016) · Disease Models & Mechanisms · doi:10.1242/dmm.023408 · Cited by 109

Gut dysbiosis as a driver in alcohol-induced liver injury

Fairfield, B., & Schnabl, B. (2020) · JHEP Reports · doi:10.1016/j.jhepr.2020.100220 · Cited by 109

Gut virome profiling identifies a widespread bacteriophage family associated with metabolic syndrome

de Jonge, P. A., Wortelboer, K., Scheithauer, T. P. M., van den Born, B. H., Zwinderman, A. H., Nóbrega, F. L., Dutilh, B. E., Nieuwdorp, M., & Herrema, H. (2022) · Nature Communications · doi:10.1038/s41467-022-31390-5 · Cited by 107

Phages in the Human Body

Navarro, F., & Muniesa, M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00566 · Cited by 115

Close Encounters of Three Kinds: Bacteriophages, Commensal Bacteria, and Host Immunity

Keen, E. C., & Dantas, G. A. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2018.05.009 · Cited by 107

Bacteriophages of the Urinary Microbiome

Miller-Ensminger, T., Garretto, A., Brenner, J., Thomas-White, K. J., Zambom, A. Z., Wolfe, A. J., & Putonti, C. (2018) · Journal of Bacteriology · doi:10.1128/jb.00738-17 · Cited by 107

Individuals at Risk for Developing Rheumatoid Arthritis Harbor Differential Intestinal Bacteriophage Communities with Distinct Metabolic Potential

Mangalea, M. R., Páez-Espino, D., Kieft, K., Chatterjee, A., Chriswell, M. E., Seifert, J. A., Feser, M. L., Demoruelle, M. K., Sakatos, A., Anantharaman, K., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.020 · Cited by 102

HIV-associated changes in the enteric microbial community: potential role in loss of homeostasis and development of systemic inflammation

Gootenberg, D. B., Paer, J. M., Luévano, J. M., & Kwon, D. S. (2016) · Current Opinion in Infectious Diseases · doi:10.1097/qco.0000000000000341 · Cited by 103

Bile acids activated receptors in inflammatory bowel disease

Biagioli, M., Marchianò, S., Carino, A., Di Giorgio, C., Santucci, L., Distrutti, E., & Fiorucci, S. (2021) · Cells · doi:10.3390/cells10061281 · Cited by 103

Hematopoiesis and the bacterial microbiome

Yan, H. H., Baldridge, M. T., & King, K. Y. (2018) · Blood · doi:10.1182/blood-2018-02-832519 · Cited by 101

Bacteriocins and Bacteriophages: Therapeutic Weapons for Gastrointestinal Diseases?

Lopetuso, L. R., Giorgio, M. E., Saviano, A., Scaldaferri, F., Gasbarrini, A., & Cammarota, G. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20010183 · Cited by 110

Microbiota and Its Role on Viral Evasion: Is It With Us or Against Us?

Domínguez-Díaz, C., García-Orozco, A., Leal, A. R., Padilla-Arellano, J. R., & Fafutis‐Morris, M. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00256 · Cited by 104

The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome

Townsend, E. M., Kelly, L., Muscatt, G., Box, J. D., Hargraves, N., Lilley, D., & Jameson, E. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.643214 · Cited by 108

Gut microbiota modulation with traditional Chinese medicine: A system biology-driven approach

Yue, S., Wang, W., Yu, J., Chen, Y., Shi, X.-Q., Yan, D., Zhou, G., Zhang, L., Wang, C., Duan, J., et al. (2019) · Pharmacological Research · doi:10.1016/j.phrs.2019.104453 · Cited by 101

MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut

Marbouty, M., Thierry, A., Millot, G. A., & Koszul, R. (2021) · eLife · doi:10.7554/elife.60608 · Cited by 103

Virus-associated organosulfur metabolism in human and environmental systems

Kieft, K., Breister, A. M., Huss, P., Linz, A. M., Zanetakos, E., Zhou, Z., Rahlff, J., Esser, S. P., Probst, A. J., Raman, S., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109471 · Cited by 95

Whole gut virome analysis of 476 Japanese revealed a link between phage and autoimmune disease

Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., Yamamoto, K., Sonehara, K., et al. (2021) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2021-221267 · Cited by 99

Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

Howe, A., Ringus, D. L., Williams, R. J., Choo, Z.-N., Greenwald, S. M., Owens, S. M., Coleman, M. L., Meyer, F., & Chang, E. B. (2015) · The ISME Journal · doi:10.1038/ismej.2015.183 · Cited by 98

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome

Casero, D., Gill, K., Sridharan, V., Koturbash, I., Nelson, G. A., Hauer‐Jensen, M., Boerma, M., Braun, J. G., & Cheema, A. K. (2017) · Microbiome · doi:10.1186/s40168-017-0325-z · Cited by 99

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis

Sinha, A., Li, Y., Mirzaei, M. K., Shamash, M., Samadfam, R., King, I. L., & Maurice, C. F. (2022) · Microbiome · doi:10.1186/s40168-022-01275-2 · Cited by 101

The Gut-Liver Axis in Cholestatic Liver Diseases

Blesl, A., & Stadlbauer, V. (2021) · Nutrients · doi:10.3390/nu13031018 · Cited by 102

Effect of intrapartum antibiotics on the intestinal microbiota of infants: a systematic review

Zimmermann, P., & Curtis, N. C. (2019) · Archives of Disease in Childhood Fetal & Neonatal · doi:10.1136/archdischild-2018-316659 · Cited by 97

Challenges in IBD Research: Environmental Triggers

Ho, S., Lewis, J. D., Mayer, E. A., Bernstein, C. N., Plevy, S. E., Chuang, E., Rappaport, S. M., Croitoru, K., Korzenik, J. R., Krischer, J. P., et al. (2019) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izz076 · Cited by 100

New Frontiers in Genetics, Gut Microbiota, and Immunity: A Rosetta Stone for the Pathogenesis of Inflammatory Bowel Disease

Zhou, M., He, J., Shen, Y., Zhang, C., Wang, J., & Chen, Y. (2017) · BioMed Research International · doi:10.1155/2017/8201672 · Cited by 97

Gut microbiome interventions in human health and diseases

Nie, P., Li, Z., Wang, Y., Zhang, Y., Zhao, M., Luo, J., Du, S., Deng, Z., Chen, J., Wang, Y., et al. (2019) · Medicinal Research Reviews · doi:10.1002/med.21584 · Cited by 94

Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection

Buttó, L. F., Schaubeck, M., & Haller, D. (2015) · Frontiers in Immunology · doi:10.3389/fimmu.2015.00555 · Cited by 97

Macrobiota — helminths as active participants and partners of the microbiota in host intestinal homeostasis

Gause, W. C., & Maizels, R. M. (2016) · Current Opinion in Microbiology · doi:10.1016/j.mib.2016.04.004 · Cited by 98

Dysregulation of Intestinal Epithelial Cell RIPK Pathways Promotes Chronic Inflammation in the IBD Gut

Garcia‐Carbonell, R., Yao, S.-J., Das, S., & Gumá, M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01094 · Cited by 92

Gut virome in inflammatory bowel disease and beyond

Tun, H. M., Peng, Y., Massimino, L., Sin, Z. Y., Parigi, T. L., Facoetti, A., Rahman, S., Danese, S., & Ungaro, F. (2023) · Gut · doi:10.1136/gutjnl-2023-330001 · Cited by 101

Protective and pro-inflammatory roles of intestinal bacteria

Webb, C. R., Koboziev, I., Furr, K. L., & Grisham, M. B. (2016) · Pathophysiology · doi:10.1016/j.pathophys.2016.02.002 · Cited by 102

Transforming medicine with the microbiome

Zmora, N., Soffer, E., & Elinav, E. (2019) · Science Translational Medicine · doi:10.1126/scitranslmed.aaw1815 · Cited by 92

Demographic and environmental drivers of metagenomic viral diversity in vampire bats

Bergner, L. M., Orton, R. J., Benavides, J. A., Becker, D. J., Tello, C., Biek, R., & Streicker, D. G. (2019) · Molecular Ecology · doi:10.1111/mec.15250 · Cited by 90

Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease

Liang, G., Conrad, M. A., Kelsen, J. R., Kessler, L. R., Breton, J., Albenberg, L. G., Marakos, S., Galgano, A. C., Devas, N., Erlichman, J., et al. (2020) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjaa094 · Cited by 94

The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome

Yu, Y., Wang, W., & Zhang, F. (2023) · Advanced Science · doi:10.1002/advs.202301097 · Cited by 105

Alteration of the Gut Microbiome in Inflammatory Bowel Disease

Andoh, A., & Nishida, A. (2023) · Digestion · doi:10.1159/000525925 · Cited by 88

Spatial disturbances in altered mucosal and luminal gut viromes of diet‐induced obese mice

Kim, M., & Bae, J. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13182 · Cited by 95

Shining Light on Human Gut Bacteriophages

Guerin, E., & Hill, C. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00481 · Cited by 88

Gut Microbiota May Play a Significant Role in the Pathogenesis of Graves' Disease

Jiang, W., Yu, X., Kosik, R. O., Song, Y., Qiao, T., Tong, J., Liu, S., Fan, S., Luo, Q., Chai, L., et al. (2020) · Thyroid · doi:10.1089/thy.2020.0193 · Cited by 94

SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination

Handley, S. A., Desai, C., Zhao, G., Droit, L., Monaco, C. L., Schroeder, A. C., Nkolola, J. P., Norman, M. E., Miller, A. D., Wang, D., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.02.010 · Cited by 89

“I will survive”: A tale of bacteriophage-bacteria coevolution in the gut

Sordi, L. D., Lourenço, M., & Debarbieux, L. (2018) · Gut Microbes · doi:10.1080/19490976.2018.1474322 · Cited by 89

Roles of the gut virome and mycobiome in faecal microbiota transplantation

Lam, S., Bai, X., Shkoporov, A. N., Park, H., Wu, X., Lan, P., & Zuo, T. (2022) · The Lancet. Gastroenterology & hepatology · doi:10.1016/s2468-1253(21)00303-4 · Cited by 89

Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome

Levy, M., Thaiss, C. A., & Elinav, E. (2015) · Genome Medicine · doi:10.1186/s13073-015-0249-9 · Cited by 94

Complexities of Gut Microbiome Dysbiosis in the Context of HIV Infection and Antiretroviral Therapy

Li, X., Armstrong, A., Neff, C. P., Shaffer, M., Lozupone, C., & Palmer, B. E. (2016) · Clinical Pharmacology & Therapeutics · doi:10.1002/cpt.363 · Cited by 93

The Gut Microbiota in Inflammatory Bowel Disease

Sheehan, D., & Shanahan, F. (2017) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2016.09.011 · Cited by 88

Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages

Mathieu, A., Dion, M. B., Deng, L., Tremblay, D. M., Moncaut, E., Shah, S. A., Stokholm, J., Krogfelt, K. A., Schjørring, S., Bisgaard, H. F., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14042-z · Cited by 84

Isolation and characterisation of ΦcrAss002, a crAss-like phage from the human gut that infects Bacteroides xylanisolvens

Guerin, E., Shkoporov, A. N., Stockdale, S. R., Colom, J., Khokhlova, E. V., Clooney, A. G., Daly, K. M., Draper, L. A., Stephens, N., Scholz, D., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01036-7 · Cited by 86

Unraveling the viral dark matter through viral metagenomics

Santiago-Rodríguez, T. M., & Hollister, E. B. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1005107 · Cited by 88

Signals triggering prophage induction in the gut microbiota

Henrot, C., & Petit, M. (2022) · Molecular Microbiology · doi:10.1111/mmi.14983 · Cited by 85

Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease

Yang, K., Wang, X., Hou, R., Lu, C., Fan, Z., Li, J., Wang, S., Xu, Y., Shen, Q., Friman, V., et al. (2023) · Microbiome · doi:10.1186/s40168-023-01463-8 · Cited by 92

Gut microbiome: a new player in gastrointestinal disease

Gorkiewicz, G., & Moschen, A. R. (2017) · Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin · doi:10.1007/s00428-017-2277-x · Cited by 95

Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host–microbe interactions

Altındiş, E., Cai, W., Sakaguchi, M., Fa, Z., GuoXiao, W., Liu, F., MEYTS, P. D., Gelfanov, V. M., Pan, H., DiMarchi, R. D., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1721117115 · Cited by 86

Inflammatory Bowel Disease: A Potential Result from the Collusion between Gut Microbiota and Mucosal Immune System

Yue, B., Luo, X., Yu, Z., Mani, S., Wang, Z., & Dou, W. (2019) · Microorganisms · doi:10.3390/microorganisms7100440 · Cited by 86

A framework for microbiome science in public health

Wilkinson, J. E., Franzosa, E. A., Everett, C., Li, C., trainees, H. R. A., Bae, S., Berzansky, I., Bhosle, A., Bjørnevik, K., Brennan, C. A., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01258-0 · Cited by 92

The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications

Bai, G.-H., Lin, S., Hsu, Y., & Chen, S.-Y. (2022) · Viruses · doi:10.3390/v14020278 · Cited by 93

Fecal microbiota profiles in treatment-naïve pediatric inflammatory bowel disease – associations with disease phenotype, treatment, and outcome

Olbjørn, C., Småstuen, M. C., Thiis‐Evensen, E., Nakstad, B., Vatn, M. H., Jahnsen, J., Ricanek, P., Vatn, S., Moen, A. E. F., Tannæs, T. M., et al. (2019) · Clinical and Experimental Gastroenterology · doi:10.2147/ceg.s186235 · Cited by 86

Mesenchymal stem cell–gut microbiota interaction in the repair of inflammatory bowel disease: an enhanced therapeutic effect

Ocansey, D. K. W., Wang, L., Wang, J., Yan, Y., Qian, H., Zhang, X., Xu, W., & Mao, F. (2019) · Clinical and Translational Medicine · doi:10.1186/s40169-019-0251-8 · Cited by 87

The healthy human virome: from virus–host symbiosis to disease

Koonin, E. V., Dolja, V. V., & Krupovìč, M. (2021) · Current Opinion in Virology · doi:10.1016/j.coviro.2021.02.002 · Cited by 86

The Interplay between Immune System and Microbiota in Inflammatory Bowel Disease: A Narrative Review

Aldars‐García, L., Marín, A. C., Chaparro, M., & Gisbert, J. P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22063076 · Cited by 91

Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants

Kaelin, E. A., Rodríguez, C., Hall-Moore, C. M., Hoffmann, J. A., Linneman, L. A., Ndao, I. M., Warner, B. B., Tarr, P. I., Holtz, L. R., & Lim, E. S. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01096-x · Cited by 85

Mouse Vendor Influence on the Bacterial and Viral Gut Composition Exceeds the Effect of Diet

Rasmussen, T. S., de Vries, L., Kot, W., Hansen, L. H., Castro-Mejía, J. L., Vogensen, F. K., Hansen, A. K., & Nielsen, D. S. (2019) · Viruses · doi:10.3390/v11050435 · Cited by 85

The role of gastrointestinal pathogens in inflammatory bowel disease: a systematic review

Axelrad, J. E., Cadwell, K., Colombel, J., & Shah, S. C. (2021) · Therapeutic Advances in Gastroenterology · doi:10.1177/17562848211004493 · Cited by 85

An Update of Research Animal Models of Inflammatory Bowel Disease

Baydi, Z., Limami, Y., Khalki, L., Zaïd, N., Naya, A., Mtairag, E. M., Oudghiri, M., & Zaid, Y. (2021) · The Scientific World JOURNAL · doi:10.1155/2021/7479540 · Cited by 86

Nanozyme engineering in structurally explicit framework: Design mechanisms and biosensing applications

Xu, Y., Huang, A., Yi, W., Chen, G., Huang, S., & Chen, G. (2023) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2023.215517 · Cited by 88

Phage Therapy in Gastrointestinal Diseases

Gutiérrez, B., & Domingo‐Calap, P. (2020) · Microorganisms · doi:10.3390/microorganisms8091420 · Cited by 89

Influenza Virus Infection Impairs the Gut’s Barrier Properties and Favors Secondary Enteric Bacterial Infection through Reduced Production of Short-Chain Fatty Acids

Sencio, V., Gallerand, A., Machado, M. G., Deruyter, L., Heumel, S., Soulard, D., Barthelemy, J., Cuinat, C., Vieira, A. T., Barthélémy, A., et al. (2021) · Infection and Immunity · doi:10.1128/iai.00734-20 · Cited by 87

The Gut Microbiome in Inflammatory Bowel Disease: Lessons Learned From Other Immune-Mediated Inflammatory Diseases

Knox, N., Forbes, J. D., Peterson, C.-L., Domselaar, G. V., & Bernstein, C. N. (2019) · The American Journal of Gastroenterology · doi:10.14309/ajg.0000000000000305 · Cited by 87

The Role of Rhizosphere Bacteriophages in Plant Health

Pratama, A. A., Terpstra, J., de Oliveria, A. L. M., & Salles, J. F. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.04.005 · Cited by 88

Gut microbiota in pathophysiology, diagnosis, and therapeutics of inflammatory bowel disease

Pandey, H., Jain, D., Tang, D. W. T., Wong, S. H., & Lal, D. (2023) · Intestinal Research · doi:10.5217/ir.2023.00080 · Cited by 95

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course

Schirmer, M., Stražar, M., Ávila-Pacheco, J., Rojas‐Tapias, D. F., Brown, E., Temple, E. R., Deik, A., Bullock, K. H., Jeanfavre, S., Pierce, K. A., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2023.12.013 · Cited by 87

The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity

Longman, R., & Littman, D. R. (2015) · Current Opinion in Rheumatology · doi:10.1097/bor.0000000000000190 · Cited by 82

Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn’s disease

Liu, T., Kern, J. T., VanDussen, K. L., Xiong, S., Kaiko, G. E., Wilen, C. B., Rajala, M. W., Caruso, R., Holtzman, M. J., Gao, F., et al. (2018) · Journal of Clinical Investigation · doi:10.1172/jci120453 · Cited by 88

Advances in the integration of metabolomics and metagenomics for human gut microbiome and their clinical applications

Puig‐Castellví, F., Pacheco‐Tapia, R., Deslande, M., Jia, M., Andrikopoulos, P., Chechi, K., Bonnefond, A., Froguel, P., & Dumas, M. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117248 · Cited by 85

Stable core virome despite variable microbiome after fecal transfer

Broecker, F., Russo, G., Klumpp, J., & Moelling, K. (2016) · Gut Microbes · doi:10.1080/19490976.2016.1265196 · Cited by 79

Bacteriophages as New Human Viral Pathogens

Tetz, G. V., & Tetz, V. (2018) · Microorganisms · doi:10.3390/microorganisms6020054 · Cited by 87

Good or bad: gut bacteria in human health and diseases

Wang, H., Wei, C.-X., Lu, M., & Zhu, L. (2018) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2018.1481350 · Cited by 90

A dysbiotic enteric virome

Kåhrström, C. T. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3442 · Cited by 1

The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice

Cao, Z., Fan, D., Sun, Y., Huang, Z., Li, Y., Su, R., Zhang, F., Li, Q., Yang, H., Zhang, F., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45794-y · Cited by 62

Characterizing the gut virome in ulcerative colitis and crohn’s disease: signatures of disease severity

Daryani, N. E., Jazayeri, S. M., Izadi, N., Ahmadi, H., Baghi, H. B., Shirmohammadi, M., Sabbaghian, M., Shekarchi, A. A., Marvi, S. S., Azadi, A., et al. (2026) · Virology Journal · doi:10.1186/s12985-026-03091-8 · Cited by 6

The Enteric Virome in Inflammatory Bowel Disease

Brooks, J., & Watson, A. J. M. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.08.022 · Cited by 7

Gut DNA virome enterotype dictates inflammation heterogeneity through tuning the phage-bacteria-sphingosine-intestine axis in Crohn's disease

Wen, W., Su, R., Liu, Y., Feng, Z., Li, Y., Li, J., Huang, Z., Zhang, F., Gao, S., Ma, Y., et al. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.01.016 · Cited by 6