Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation
Open accessAbstract
Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.
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Intestinal mucosal resurfacing is a technique that targets the duodenal surface in order to improve the intestinal barrier.
“Intestinal mucosal resurfacing (124) is a technique that targets the duodenal surface in order to improve the intestinal barrier.”
From Modulation of the gut–brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis (2023) · cites this paper as [124]
Oral compound phage-targeted therapy can inhibit human intestinal microbiota symbiosis, improve intestinal inflammation, and effectively avoid antibiotic resistance.
“Federici et al. (124) demonstrated that oral compound phage-targeted therapy can inhibit human intestinal microbiota symbiosis, improve intestinal inflammation, and effectively avoid antibiotic resistance.”
From Modulation of the gut–brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis (2023) · cites this paper as [124]
Intestinal mucosal resurfacing is currently used in patients with type 2 diabetes to improve the proliferation of enteroendocrine cells and endocrine cells, ultimately improving blood glucose levels.
“This technique is currently used in patients with type 2 diabetes to improve the proliferation of enteroendocrine cells and endocrine cells, ultimately improving blood glucose levels.”
From Modulation of the gut–brain axis via the gut microbiota: a new era in treatment of amyotrophic lateral sclerosis (2023) · cites this paper as [124]
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
fastp: an ultra-fast all-in-one FASTQ preprocessor
(2018) · doi:10.1093/bioinformatics/bty560 · Cited by 29,721 · see citing works
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 25,691 · see citing works
Improved metagenomic analysis with Kraken 2
Wood, D. E., Lu, J., & Langmead, B. (2019) · Genome biology · doi:10.1186/s13059-019-1891-0 · Cited by 7,173 · see citing works
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975 · see citing works
CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes
Barrangou, R., Fremaux, C., Deveau, H., Richards, M., Boyaval, P., Moineau, S., Romero, D. A., & Horvath, P. (2007) · Science · doi:10.1126/science.1138140 · Cited by 6,304 · see citing works
Sensitive protein alignments at tree-of-life scale using DIAMOND
Buchfink, B., Reuter, K., & Drost, H.-G. (2021) · Nature Methods · doi:10.1038/s41592-021-01101-x · Cited by 5,097 · see citing works
The Pfam protein families database in 2019
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602 · see citing works
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555 · see citing works
CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database
Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202 · 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
PANTHER: A Library of Protein Families and Subfamilies Indexed by FunctionPreprint
Thomas, P. D., Campbell, M. J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., & Narechania, A. (2003) · Genome Research · doi:10.1101/gr.772403 · Cited by 2,912 · see citing works
Brettin, T. S., Davis, J. J., Disz, T. L., Edwards, R. A., Gerdes, S., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., et al. (2015) · Scientific Reports · doi:10.1038/srep08365 · Cited by 2,830 · see citing works
The global burden of IBD: from 2015 to 2025
Kaplan, G. G. (2015) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2015.150 · Cited by 2,639 · see citing works
Bacteriophage resistance mechanisms
Labrie, S. J., Samson, J. E., & Moineau, S. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2315 · Cited by 2,405 · see citing works
Bracken: estimating species abundance in metagenomics data
(2016) · doi:10.7717/peerj-cs.104 · Cited by 2,333 · see citing works
Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H., & the UniProt Consortium (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu739 · Cited by 1,928 · see citing works
The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead
Kostic, A. D., Xavier, R. J., & Gevers, D. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.02.009 · Cited by 1,789 · 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
Feldgarden, M., Brover, V. V., González‐Escalona, N., Frye, J. G., Haendiges, J., Haft, D. H., Hoffmann, M., Pettengill, J., Prasad, A. B., Tillman, G. E., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-91456-0 · Cited by 1,697 · see citing works
Species-level functional profiling of metagenomes and metatranscriptomes
Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693 · see citing works
Deatherage, D. E., & Barrick, J. E. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0554-6_12 · Cited by 1,671 · see citing works
Sulakvelidze, A., Alavidze, Z., & Morris, J. G. (2001) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.45.3.649-659.2001 · Cited by 1,569 · see citing works
Feldgarden, M., Brover, V. V., Haft, D. H., Prasad, A. B., Slotta, D. J., Tolstoy, I., Tyson, G. H., Zhao, S., Hsu, C.-H., McDermott, P. F., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00483-19 · Cited by 1,436 · see citing works
Dedrick, R. M., Guerrero-Bustamante, C. A., Garlena, R. A., Russell, D. A., Ford, K., Harris, K., Gilmour, K. C., Soothill, J. S., Jacobs‐Sera, D., Schooley, R. T., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0437-z · Cited by 1,418 · see citing works
Wirbel, J., Pyl, P. T., Kartal, E., Zych, K., Kashani, A., Milanese, A., Fleck, J. S., Voigt, A. Y., Palleja, A., Ponnudurai, R., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0406-6 · Cited by 1,373 · 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
Paramsothy, S., Kamm, M. A., Kaakoush, N. O., Walsh, A. J., van den Bogaerde, J., Samuel, D., Leong, R. W. L., Connor, S., Ng, W., Paramsothy, R., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)30182-4 · Cited by 1,276 · see citing works
Systematic discovery of antiphage defense systems in the microbial pangenome
Doron, S., Melamed, S., Ofir, G., Leavitt, A., Lopatina, A., Keren, M., Amitai, G., & Sorek, R. (2018) · Science · doi:10.1126/science.aar4120 · Cited by 1,190 · see citing works
Self-citationPowrie, F., Leach, M. W., Mauze, S., Menon, S., Barcomb Caddle, L., & Coffman, R. L. (1994) · Immunity · doi:10.1016/1074-7613(94)90045-0 · Cited by 1,146 · see citing works
Lam, M. M. C., Wick, R. R., Watts, S. C., Cerdeira, L., Wyres, K. L., & Holt, K. E. (2021) · Nature Communications · doi:10.1038/s41467-021-24448-3 · Cited by 1,093 · see citing works
Atarashi, K., Suda, W., Luo, C., Kawaguchi, T., Motoo, I., Narushima, S., Kiguchi, Y., Yasuma, K., Watanabe, E., Tanoue, T., et al. (2017) · Science · doi:10.1126/science.aan4526 · Cited by 957 · see citing works
Self-citationEnvironmental triggers in IBD: a review of progress and evidence
Ananthakrishnan, A. N., Bernstein, C. N., Iliopoulos, D., Macpherson, A., Neurath, M. F., Ali, R. A. R., Vavricka, S. R., & Fiocchi, C. (2018) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2017.136 · Cited by 948 · see citing works
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
Davis, J. J., Wattam, A. R., Aziz, R. K., Brettin, T. S., Butler, R. M., Butler, R., Chlenski, P., Conrad, N. R., Dickerman, A. W., Dietrich, E. M., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz943 · Cited by 880 · see citing works
Diet-microbiota interactions and personalized nutrition
Kolodziejczyk, A. A., Zheng, D., & Elinav, E. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0256-8 · Cited by 879 · see citing works
Self-citationPresence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease
Darfeuille–Michaud, A., Neut, C., Barnich, N., Lederman, E., Martino, P. D., Desreumaux, P., Gambiez, L. P., Joly, B., Cortot, A., & Colombel, J.-F. (1998) · Gastroenterology · doi:10.1016/s0016-5085(98)70019-8 · Cited by 859 · see citing works
Rath, H. C., Herfarth, H. H., Ikeda, J. S., Grenther, W. B., Hamm, T. E., Balish, E., Taurog, J. D., Hammer, R. E., Wilson, K. H., & Sartor, R. B. (1996) · Journal of Clinical Investigation · doi:10.1172/jci118878 · Cited by 833 · see citing works
Self-citationLewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works
The Impact of Food Bioactives on Health
Verhoeckx, K. C. M., Cotter, P., López-Expósito, I., Kleiveland, C., Lea, T., Mackie, A. R., Requena, T., Swiatecka, D., & Wichers, H. J. (2015) · Springer eBooks · doi:10.1007/978-3-319-16104-4 · Cited by 816 · see citing works
Host–microbiota interactions in inflammatory bowel disease
Caruso, R., Lo, B. C., & Núñez, G. (2020) · Nature reviews. Immunology · doi:10.1038/s41577-019-0268-7 · Cited by 776 · see citing works
Mining the Human Gut Microbiota for Immunomodulatory Organisms
Geva-Zatorsky, N., Sefik, E., Kua, L., Pasman, L., Tan, T. G., Ortiz-Lopez, A., Yanortsang, T. B., Yang, L., Jupp, R., Mathis, D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.01.022 · Cited by 762 · see citing works
Experimental Models of Inflammatory Bowel Diseases
Kiesler, P., Fuss, I. J., & Strober, W. (2015) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2015.01.006 · Cited by 719 · see citing works
Gut microbiome pattern reflects healthy ageing and predicts survival in humans
Wilmanski, T. M., Diener, C., Rappaport, N., Patwardhan, S., Wiedrick, J. T., Lapidus, J., Earls, J. C., Zimmer, A., Glusman, G., Robinson, M., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-021-00348-0 · Cited by 693 · see citing works
Garneau, J. R., Depardieu, F., Fortier, L., Bikard, D., & Monot, M. (2017) · Scientific Reports · doi:10.1038/s41598-017-07910-5 · Cited by 690 · see citing works
The Intermucosal Connection between the Mouth and Gut in Commensal Pathobiont-Driven Colitis
Kitamoto, S., Nagao‐Kitamoto, H., Jiao, Y., Gillilland, M. G., Hayashi, A., Imai, J., Sugihara, K., Miyoshi, M., Brazil, J. C., Kuffa, P., et al. (2020) · Cell · doi:10.1016/j.cell.2020.05.048 · Cited by 685 · see citing works
Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis
Gogokhia, L., Buhrke, K., Bell, R. S., Hoffman, B., Brown, D. G., Hanke‐Gogokhia, C., Ajami, N. J., Wong, M. C., Ghazaryan, A., Valentine, J. F., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.008 · Cited by 613 · see citing works
Targeting mechanisms of tailed bacteriophages
Nóbrega, F. L., Vlot, M., de Jonge, P. A., Dreesens, L. L., Beaumont, H. J. E., Lavigne, R., Dutilh, B. E., & Brouns, S. J. J. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0070-8 · Cited by 601 · see citing works
NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer
Couturier-Maillard, A., Sécher, T., Rehman, A., Normand, S., Arcangelis, A. D., Häsler, R., Huot, L., Grandjean, T., Bressenot, A., Delanoye, A., et al. (2013) · Journal of Clinical Investigation · doi:10.1172/jci62236 · Cited by 571 · see citing works
Colman, R. J., & Rubin, D. T. (2014) · Journal of Crohn's and Colitis · doi:10.1016/j.crohns.2014.08.006 · Cited by 475 · see citing works
Schaubeck, M., Clavel, T., Calasan, J., Lagkouvardos, I., Haange, S. B., Jehmlich, N., Basic, M., Dupont, A., Hornef, M., Bergen, M. V., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-309333 · Cited by 447 · see citing works
Paramsothy, S., Paramsothy, R., Rubin, D. T., Kamm, M. A., Kaakoush, N. O., Mitchell, H. M., & Castaño-Rodríguez, N. (2017) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjx063 · Cited by 436 · see citing works
Yang, B.-H., Hagemann, S., Mamareli, P., Lauer, U., Hoffmann, U., Beckstette, M., Föhse, L., Prinz, I., Pezoldt, J., Suerbaum, S., et al. (2015) · Mucosal Immunology · doi:10.1038/mi.2015.74 · Cited by 435 · see citing works
Kim, S. C., Tonkonogy, S. L., Albright, C. A., Tsang, J., Balish, E., Braun, J., Huycke, M. M., & Sartor, R. B. (2005) · Gastroenterology · doi:10.1053/j.gastro.2005.02.009 · Cited by 433 · see citing works
Self-citationQuantifying drivers of antibiotic resistance in humans: a systematic review
Chatterjee, A., Modarai, M., Naylor, N. R., Boyd, S. E., Atun, R. A., Barlow, J. G., Holmes, A. H., Johnson, A. P., & Robotham, J. V. (2018) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(18)30296-2 · Cited by 388 · see citing works
Saint-Antoine IBD Network, Sokol, H., Landman, C., Seksik, P., Berard, L., Montil, M., Nion-Larmurier, I., Bourrier, A., Le Gall, G., Lalande, V., et al. (2020) · Microbiome · doi:10.1186/s40168-020-0792-5 · Cited by 378 · see citing works
Self-citationPathogenesis of Helicobacter pylori infection
Camilo, V., Sugiyama, T., & Touati, E. (2017) · Helicobacter · doi:10.1111/hel.12405 · Cited by 377 · see citing works
High resolution colonoscopy in live mice
Becker, C., Fantini, M. C., & Neurath, M. F. (2006) · Nature Protocols · doi:10.1038/nprot.2006.446 · Cited by 369 · see citing works
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
Hockenberry, A. J., & Wilke, C. O. (2021) · PeerJ · doi:10.7717/peerj.11396 · Cited by 338 · see citing works
Dianda, L., Hanby, A., Wright, N. A., Sebesteny, A., Hayday, A., & Owen, M. J. (1997) · Europe PMC (PubMed Central) · Cited by 337 · see citing works
Phage therapy as a potential solution in the fight against AMR: obstacles and possible futures
Brives, C., & Pourraz, J. (2020) · Humanities and Social Sciences Communications · doi:10.1057/s41599-020-0478-4 · Cited by 337 · see citing works
DISARM is a widespread bacterial defence system with broad anti-phage activities
Ofir, G., Melamed, S., Sberro, H., Mukamel, Z., Silverman, S., Yaakov, G., Doron, S., & Sorek, R. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0051-0 · Cited by 333 · see citing works
Self-citationHigh-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
Kaminski, J., Gibson, M. K., Franzosa, E. A., Segata, N., Dantas, G. A., & Huttenhower, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004557 · Cited by 325 · see citing works
Treatment of ulcerative colitis by implantation of normal colonic flora
Bennet, J., & Brinkman, M. (1989) · The Lancet · doi:10.1016/s0140-6736(89)91183-5 · Cited by 304 · see citing works
Mammalian Host-Versus-Phage immune response determines phage fate in vivo
Hodyra-Stefaniak, K., Miernikiewicz, P., Drapała, J., Drab, M., Jończyk-Matysiak, E., Lecion, D., Kaźmierczak, Z., Beta, W., Majewska, J., Harhala, M., et al. (2015) · Scientific Reports · doi:10.1038/srep14802 · Cited by 302 · see citing works
Cui, B., Feng, Q., Wang, H., Wang, M., Peng, Z., Li, P., Huang, G., Liu, Z., Wu, P., Fan, Z., et al. (2015) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.12727 · Cited by 298 · see citing works
Nonredundant Roles for B Cell-Derived IL-10 in Immune Counter-Regulation
Madan, R., Demircik, F., Surianarayanan, S., Allen, J. L., Divanovic, S., Trompette, A., Yogev, N., Gu, Y., Khodoun, M. V., Hildeman, D. A., et al. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0900185 · Cited by 295 · see citing works
Eskenazi, A., Lood, C., Wubbolts, J. M., Hites, M., Balarjishvili, N., Leshkasheli, L., Askilashvili, L., Kvachadze, L. I., van Noort, V., Wagemans, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27656-z · Cited by 288 · see citing works
Schirmer, M., Denson, L. A., Vlamakis, H. C., Franzosa, E. A., Thomas, S., Gotman, N., Rufo, P. A., Baker, S. S., Sauer, C. G., Markowitz, J. F., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.09.009 · Cited by 287 · see citing works
Hydrogen storage in incompletely etched multilayer Ti2CTx at room temperature
Liu, S., Liu, J., Liu, X., Shang, J., Li, X., Yu, R., & Shui, J. (2021) · Nature Nanotechnology · doi:10.1038/s41565-020-00818-8 · Cited by 282 · see citing works
Thia, K. T. J., Mahadevan, U., Feagan, B. G., Wong, C. J., Cockeram, A. W., Bitton, A., Bernstein, C. N., & Sandborn, W. J. (2008) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20608 · Cited by 276 · see citing works
Lood, R., Winer, B. Y., Pelzek, A. J., Díez‐Martínez, R., Thandar, M., Euler, C. W., Schuch, R., & Fischetti, V. A. (2015) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.04641-14 · Cited by 272 · see citing works
PHACTS, a computational approach to classifying the lifestyle of phages
McNair, K. A., Bailey, B., & Edwards, R. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts014 · Cited by 269 · see citing works
Oral T4-like phage cocktail application to healthy adult volunteers from Bangladesh
Sarker, S. A., McCallin, S. E., Barretto, C., Berger, B. W., Pittet, A.-C., Sultana, S., Krause, L., Huq, S., Bibiloni, R., Bruttin, A., et al. (2012) · Virology · doi:10.1016/j.virol.2012.09.002 · Cited by 240 · see citing works
Park, J. C., & Im, S. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-0473-2 · Cited by 217 · see citing works
Ayres, J. S., Trinidad, N. J., & Vance, R. E. (2012) · Nature Medicine · doi:10.1038/nm.2729 · Cited by 213 · see citing works
Watanabe, R., Matsumoto, T., Sano, G., Ishii, Y., Tateda, K., Sumiyama, Y., Uchiyama, J., Sakurai, S., Matsuzaki, S., Imai, S., et al. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00635-06 · Cited by 206 · see citing works
5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis
Xu, J., Chen, N., Wu, Z., Song, Y., Zhang, Y., Wu, N., Zhang, F., Ren, X., & Liu, Y. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01274 · Cited by 186 · see citing works
The Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)
de Wiele, T. V., den Abbeele, P. V., Ossieur, W., Possemiers, S., & Marzorati, M. (2015) · Springer eBooks · doi:10.1007/978-3-319-16104-4_27 · Cited by 185 · see citing works
Diet influences the functions of the human intestinal microbiome
Angelis, M. D., Ferrocino, I., Calabrese, F. M., Filippis, F. D., Cavallo, N., Siragusa, S., Rampelli, S., Cagno, R. D., Rantsiou, K., Vannini, L., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-61192-y · Cited by 177 · see citing works
Prantera, C., Lochs, H. H., Grimaldi, M., Danese, S., Scribano, M. L., & Gionchetti, P. (2011) · Gastroenterology · doi:10.1053/j.gastro.2011.11.032 · Cited by 174 · see citing works
Bacteriophage Therapy: Developments and Directions
Nikolich, M. P., & Filippov, A. A. (2020) · Antibiotics · doi:10.3390/antibiotics9030135 · Cited by 168 · see citing works
Mishima, Y., Oka, A., Liu, B., Herzog, J. W., Eun, C. S., Fan, T.-J., Bulik-Sullivan, E., Carroll, I. M., Hansen, J. J., Chen, L., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci93820 · Cited by 166 · see citing works
Self-citationSeishima, J., Iida, N., Kitamura, K., Yutani, M., Wang, Z., Seki, A., Yamashita, T., Sakai, Y., Honda, M., Yamashita, T., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1879-9 · Cited by 165 · see citing works
Age and the aging process significantly alter the small bowel microbiome
Leite, G., Pimentel, M., Barlow, G. M., Chang, C. Y.-Y., Hosseini, A., Wang, J., Parodi, G., Sedighi, R., Rezaie, A. R., & Mathur, R. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109765 · Cited by 158 · see citing works
Effects of metabolites derived from gut microbiota and hosts on pathogens
Li, Z., Quan, G., Jiang, X., Yang, Y., Ding, X., Zhang, D., Wang, X., Hardwidge, P. R., Ren, W., & Zhu, G. (2018) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2018.00314 · Cited by 157 · see citing works
Strain profiling and epidemiology of bacterial species from metagenomic sequencing
Albanese, D., & Donati, C. (2017) · Nature Communications · doi:10.1038/s41467-017-02209-5 · Cited by 129 · see citing works
Host–microbiota interactions in inflammatory bowel disease
Neurath, M. F. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0248-1 · Cited by 129 · see citing works
Altered gut microbial metabolism of essential nutrients in primary sclerosing cholangitis
Kummen, M., Thingholm, L. B., Rühlemann, M. C., Holm, K., Hansen, S. H., Moitinho-Silva, L., Liwinski, T., Zenouzi, R., Storm-Larsen, C., Midttun, Ø., et al. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.12.058 · Cited by 129 · see citing works
Self-citationJun, J. W., Shin, T. H., Kim, J. H., Shin, S. P., Han, J. E., Heo, G. J., Zoysa, M. D., Shin, G. W., Chai, J. Y., & Park, S. C. (2014) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiu059 · Cited by 126 · see citing works
Eun, C. S., Mishima, Y., Wohlgemuth, S., Liu, B., Bower, M., Carroll, I. M., & Sartor, R. B. (2014) · Infection and Immunity · doi:10.1128/iai.01513-13 · Cited by 124 · see citing works
Self-citationFang, H., Fu, L., & Wang, J. (2018) · BioMed Research International · doi:10.1155/2018/8941340 · Cited by 123 · see citing works
Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis
Shi, Y., Dong, Y., Huang, W., Zhu, D., Mao, H., & Su, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0157259 · Cited by 117 · see citing works
Arango-Argoty, G., Dai, D., Pruden, A. J., Vikesland, P. J., Heath, L. S., & Zhang, L. (2019) · Microbiome · doi:10.1186/s40168-019-0703-9 · Cited by 117 · see citing works
Örmälä, A.-M., & Jalasvuori, M. (2013) · Bacteriophage · doi:10.4161/bact.24219 · Cited by 103 · see citing works
Detection of enterotoxigenic Bacteroides fragilis in patients with ulcerative colitis
Zamani, S., Hesam-Shariati, S., Zali, M. R., Aghdaei, H. A., Asiabar, A. S., Bokaie, S., Nomanpour, B., Sechi, L. A., & Feizabadi, M. M. (2017) · Gut Pathogens · doi:10.1186/s13099-017-0202-0 · Cited by 102 · see citing works
Fecal microbial transplant via nasogastric tube for active pediatric ulcerative colitis
Suskind, D. L., Singh, N., Nielson, H., & Wahbeh, G. (2015) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0000000000000544 · Cited by 99 · see citing works
Majewska, J., Kaźmierczak, Z. M., Lahutta, K., Lecion, D., Szymczak, A., Miernikiewicz, P., Drapała, J., Harhala, M. A., Marek-Bukowiec, K., Jędruchniewicz, N., et al. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02607 · Cited by 97 · see citing works
He, Z., Li, P., Zhu, J., Cui, B., Xu, L., Xiang, J., Zhang, T., Long, C., Huang, G., Ji, G., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-04984-z · Cited by 94 · see citing works
Elhenawy, W., Tsai, C. N., & Coombes, B. K. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2018.12.010 · Cited by 91 · see citing works
Information Phage Therapy Research Should Report
Abedon, S. T. (2017) · Pharmaceuticals · doi:10.3390/ph10020043 · Cited by 81 · see citing works
Eri, R. D., McGuckin, M. A., & Wadley, R. B. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-527-5_19 · Cited by 73 · see citing works
Elhenawy, W., Hordienko, S., Gould, S., Oberc, A. M., Tsai, C. N., Hubbard, T. P., Waldor, M. K., & Coombes, B. K. (2021) · Nature Communications · doi:10.1038/s41467-021-22306-w · Cited by 68 · see citing works
Designing P. aeruginosa synthetic phages with reduced genomes
Pires, D. P., Monteiro, R. C. P., Mil‐Homens, D., Fialho, A. M., Lu, T. K., & Azeredo, J. (2021) · Scientific Reports · doi:10.1038/s41598-021-81580-2 · Cited by 65 · see citing works
Hyoju, S. K., Zaborin, A., Keskey, R. C., Sharma, A., Arnold, W., van den Berg, F. F., Kim, S. M., Gottel, N., Bethel, C., Charnot‐Katsikas, A., et al. (2019) · mBio · doi:10.1128/mbio.00903-19 · Cited by 50 · see citing works
Mishima, Y., Liu, B., Hansen, J. J., & Sartor, R. B. (2015) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2015.01.002 · Cited by 42 · see citing works
Self-citationSoares, F. S., AMARAL, F. C., Silva, N. L. C., Valente, M. R., Santos, L. K. R., Yamashiro, L. H., Scheffer, M. C., Castanheira, F. V. S., Ferreira, R. G., Gehrke, L., et al. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.01890 · Cited by 40 · see citing works
Swidsinski, A. V., Loening-Baucke, V. A., Bengmark, S., Scholze, J. E., & Dörffel, Y. (2007) · Archives of Medical Research · doi:10.1016/j.arcmed.2007.08.001 · Cited by 39 · see citing works
van de Wijgert, J. H. H. M., Verwijs, M. C., Gill, A. C., Borgdorff, H., van der Veer, C., & Mayaud, P. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00129 · Cited by 39 · see citing works
Fecal Microbiota Transplantation as a Novel Therapy for Ulcerative Colitis
Sun, D., Li, W., Li, S., Cen, Y., Xu, Q., Li, Y., Sun, Y., Qi, Y., Lin, Y., Yang, T., et al. (2016) · Medicine · doi:10.1097/md.0000000000003765 · Cited by 35 · see citing works
Structure of the mannose transporter of the bacterial phosphotransferase system
Liu, X., Zeng, J., Huang, K., & Wang, J. (2019) · Cell Research · doi:10.1038/s41422-019-0194-z · Cited by 33 · see citing works
Smith, D. R., Temime, L., & Opatowski, L. (2021) · eLife · doi:10.7554/elife.68764 · Cited by 30 · see citing works
Manipulating the Microbiome With Fecal Transplantation to Treat Ulcerative Colitis
Kelly, C. R., & Ananthakrishnan, A. N. (2019) · JAMA · doi:10.1001/jama.2018.20397 · Cited by 28 · see citing works
Dang, X., Wang, Q., Zhao, Y., Sun, L., & Yang, W. (2020) · BMC Gastroenterology · doi:10.1186/s12876-020-01548-w · Cited by 15 · see citing works
Tocia, C., Dumitru, I. M., Alexandrescu, L., Petcu, L. C., & Dumitru, E. (2021) · Medicine · doi:10.1097/md.0000000000024059 · Cited by 12 · see citing works
Tran, V., Phan, J., Nulsen, B., Huang, L., Kaneshiro, M., Weiss, G. A., Ho, W. W., Sack, J. L., Ha, C. Y., Uslan, D. Z., et al. (2018) · ACG Case Reports Journal · doi:10.14309/crj.2018.97 · Cited by 9 · see citing works
B-Cell Commitment to IL-10 Production: The VertX Il10egfp Mouse
Oka, A., Liu, B., Herzog, J., & Sartor, R. B. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1237-8_19 · Cited by 3 · see citing works
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Gut microbiota in colorectal cancer development and therapy
Wong, C. C., & Yu, J. (2023) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-023-00766-x · Cited by 751 · see citing works
Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice
Gencay, Y. E., Jasinskytė, D., Robert, C., Semsey, S., Martínez, V., Petersen, A. Ø., Brunner, K., de Santiago Torio, A., Salazar, A., Turcu, I. C., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-023-01759-y · Cited by 282 · see citing works
Microbiome-based interventions to modulate gut ecology and the immune system
Hitch, T. C. A., Hall, L. J., Walsh, S. K., Leventhal, G. E., Slack, E. M. C., de Wouters, T., Walter, J., & Clavel, T. (2022) · Mucosal Immunology · doi:10.1038/s41385-022-00564-1 · Cited by 251 · see citing works
A Review of Gut Microbiota‐Derived Metabolites in Tumor Progression and Cancer Therapy
Yang, Q., Wang, B., Zheng, Q., Li, H., Meng, X., Zhou, F., & Zhang, L. (2023) · Advanced Science · doi:10.1002/advs.202207366 · Cited by 249 · see citing works
Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities
Iliev, I. D., Ananthakrishnan, A. N., & Guo, C.-J. (2025) · Nature Reviews Microbiology · doi:10.1038/s41579-025-01163-0 · Cited by 249 · see citing works
Gilliland, A., Chan, J. J., Wolfe, T. J. D., Yang, H., & Vallance, B. A. (2023) · Gastroenterology · doi:10.1053/j.gastro.2023.09.019 · Cited by 229 · see citing works
Sasso, J. M., Ammar, R. M., Tenchov, R., Lemmel, S. A., Kelber, O., Grieswelle, M., & Zhou, Q. A. (2023) · ACS Chemical Neuroscience · doi:10.1021/acschemneuro.3c00127 · Cited by 218 · see citing works
Another renaissance for bile acid gastrointestinal microbiology
Ridlon, J. M., & Gaskins, H. R. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00896-2 · Cited by 193 · see citing works
Implications of the changing epidemiology of inflammatory bowel disease in a changing world
Agrawal, M., & Jess, T. (2022) · United European Gastroenterology Journal · doi:10.1002/ueg2.12317 · Cited by 187 · see citing works
Utilization of the microbiome in personalized medicine
Ratiner, K., Ciocan, D. M., Abdeen, S. K., & Elinav, E. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00998-9 · Cited by 179 · see citing works
Self-citationNickols, W. A., Kuntz, T. M., Shen, J., Maharjan, S., Mallick, H., Franzosa, E. A., Thompson, K. N., Nearing, J. T., & Huttenhower, C. (2026) · Nature Methods · doi:10.1038/s41592-025-02923-9 · Cited by 192 · see citing works
Gan, L., Feng, Y., Du, B., Fu, H., Tian, Z., Xue, G., Yan, C., Cui, X., Zhang, R., Cui, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39028-w · Cited by 162 · see citing works
Wu, D., Jin, Y., Xing, Y., Abate, M. D., Abbasian, M., Abbasi‐Kangevari, M., Abbasi-Kangevari, Z., Abd-Allah, F., Abdelmasseh, M., Abdollahifar, M.-A., et al. (2023) · EClinicalMedicine · doi:10.1016/j.eclinm.2023.102193 · Cited by 146 · see citing works
Phages overcome bacterial immunity via diverse anti-defence proteins
(2023) · doi:10.1038/s41586-023-06869-w · Cited by 138 · see citing works
Self-citationNoninvasive, microbiome-based diagnosis of inflammatory bowel disease
Zheng, J., Sun, Q., Zhang, M., Liu, C., Su, Q., Zhang, L., Xu, Z., Lu, W., Ching, J. Y. L., Tang, W., et al. (2024) · Nature Medicine · doi:10.1038/s41591-024-03280-4 · Cited by 144 · see citing works
Intestinal bacteria and colorectal cancer: etiology and treatment
Dougherty, M. W., & Jobin, C. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2185028 · Cited by 138 · see citing works
Nemet, I., Li, X. S., Haghikia, A., Li, L., Wilcox, J. D., Romano, K. A., Buffa, J. A., Witkowski, M., Demuth, I., König, M., et al. (2023) · European Heart Journal · doi:10.1093/eurheartj/ehad333 · Cited by 128 · see citing works
Translating phage therapy into the clinic: Recent accomplishments but continuing challenges
Fabijan, A. P., Iredell, J. R., Danis-Wlodarczyk, K. M., Kebriaei, R., & Abedon, S. T. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002119 · Cited by 126 · see citing works
Yan, Q., Li, S., Yan, Q., Huo, X., Wang, C., Wang, X., Sun, Y., Zhao, W., Yu, Z., Zhang, Y., et al. (2024) · Cell · doi:10.1016/j.cell.2024.04.043 · Cited by 121 · see citing works
Ichikawa, M., Nakamoto, N., Kredo‐Russo, S., Weinstock, E., Weiner, I. N., Khabra, E., Ben-Ishay, N., Inbar, D., Kowalsman, N., Mordoch, R., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-39029-9 · Cited by 111 · see citing works
Self-citationIntracellular bacteria in cancer—prospects and debates
Schorr, L., Mathies, M., Elinav, E., & Puschhof, J. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00446-9 · Cited by 113 · see citing works
Self-citationBerkson, J. D., Wate, C. E., Allen, G. B., Schubert, A. M., Dunbar, K. E., Coryell, M. P., Sava, R. L., Gao, Y. S., Hastie, J. L., Smith, E. M., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-47192-w · Cited by 109 · see citing works
Enhancing intestinal barrier efficiency: A novel metabolic diseases therapy
Zhang, Y., Xiao, Z., Yu, X., Novák, P., Gui, Q., & Yin, K. (2023) · Frontiers in Nutrition · doi:10.3389/fnut.2023.1120168 · Cited by 110 · see citing works
The emerging role of the gut microbiota and its application in inflammatory bowel disease
Xiu, W., Peng, J., Cai, P., Xia, Y., Yi, C., Shang, A., Akanyibah, F. A., & Mao, F. (2024) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2024.117302 · Cited by 105 · see citing works
Fu, Y., Zhao, X., Wang, L., Li, K., Jiang, N., Zhang, S., Wang, R., Zhao, Y., & Yang, W. M. (2024) · Advanced Materials · doi:10.1002/adma.202309972 · Cited by 103 · see citing works
Lau, H. C.-H., Zhang, X., & Yu, J. (2025) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-025-01089-1 · Cited by 112 · see citing works
Gut–liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice
Wang, X., Fang, Y., Liang, W., Cai, Y., Wong, C. C., Wang, J., Wang, N., Lau, H. C.-H., Jiao, Y., Zhou, X., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-024-01890-9 · Cited by 102 · see citing works
Keung, W.-S., Zhang, W.-H., Luo, H.-Y., Chan, K.-C., Chan, Y.-M., & Xu, J. (2025) · Carbohydrate Polymers · doi:10.1016/j.carbpol.2024.123209 · Cited by 100 · see citing works
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 95 · see citing works
Clinical translation of microbiome research
Gilbert, J. A., Azad, M. B., Bäckhed, F., Blaser, M. J., Byndloss, M. X., Chiu, C. Y., Chu, H., Dugas, L. R., Elinav, E., Gibbons, S. M., et al. (2025) · Nature Medicine · doi:10.1038/s41591-025-03615-9 · Cited by 103 · see citing works
Self-citationThe 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 94 · see citing works
Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites
Kaplina, A., Kononova, S., Zaikova, E. K., Pervunina, T. M., Petrova, N. A., & Sitkin, S. I. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032471 · Cited by 95 · see citing works
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 82 · see citing works
Metabolic ecology of microbiomes: Nutrient competition, host benefits, and community engineering
Bakkeren, E., Piskovsky, V., & Foster, K. R. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.05.013 · Cited by 91 · see citing works
Microbiota therapeutics for inflammatory bowel disease: the way forward
Bethlehem, L., Estevinho, M. M., Grinspan, A. M., Magro, F., Faith, J. J., & Colombel, J. (2024) · The Lancet. Gastroenterology & hepatology · doi:10.1016/s2468-1253(23)00441-7 · Cited by 80 · see citing works
Microbiota-immune-brain interactions: A lifespan perspective
Ratsika, A., Cruz-Pereira, J. S., Lynch, C. M. K., Clarke, G. A., & Cryan, J. F. (2022) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2022.102652 · Cited by 78 · see citing works
Smoking-induced microbial dysbiosis in health and disease
Shapiro, H., Goldenberg, K., Ratiner, K., & Elinav, E. (2022) · Clinical Science · doi:10.1042/cs20220175 · Cited by 70 · see citing works
Self-citationSpiga, L., Fansler, R. T., Perera, Y. R., Shealy, N. G., Munneke, M. J., David, H. E., Torres, T. P., Lemoff, A. S., Ran, X., Richardson, K. L., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.08.018 · Cited by 71 · see citing works
Kuang, X., Liu, Y., Luo, H., Li, Q., Wu, F. Q., Fan, C., & Liu, J. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c10015 · Cited by 69 · see citing works
Akiyama, S., Nishijima, S., Kojima, Y., Kimura, M., Ohsugi, M., Ueki, K., Mizokami, M., Hattori, M., Tsuchiya, K., Uemura, N., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54797-8 · Cited by 69 · see citing works
Microbiome-phage interactions in inflammatory bowel disease
Federici, S., Kviatcovsky, D., Valdés‐Mas, R., & Elinav, E. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2022.08.027 · Cited by 67 · see citing works
Self-citationSaftien, A., Puschhof, J., & Elinav, E. (2023) · Gut · doi:10.1136/gutjnl-2022-327952 · Cited by 67 · see citing works
Self-citationZhou, Z., Wang, Y., Sun, S., Zhang, K., Wang, L., Zhao, H., & Zhang, Y. (2023) · Journal of Ethnopharmacology · doi:10.1016/j.jep.2023.116716 · Cited by 67 · see citing works
Li, C., Zhang, P., Xie, Y., Wang, S., Guo, M., Wei, X., Zhang, K., Cao, D., Zhou, R., Wang, S., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.04.020 · Cited by 65 · see citing works
Endogenous ethanol production in health and disease
Meijnikman, A. S., Nieuwdorp, M., & Schnabl, B. (2024) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-024-00937-w · Cited by 69 · see citing works
Koncz, M., Stirling, T., Mehdi, H. H., Méhi, O., Eszenyi, B., Asbóth, A., Apjok, G., Tóth, Á., Orosz, L. I., Vásárhelyi, B. M., et al. (2024) · Cell · doi:10.1016/j.cell.2024.09.009 · Cited by 67 · see citing works
Implications of gut microbiota-mediated epigenetic modifications in intestinal diseases
Zhang, Q., Liu, Y., Li, Y., Bai, G., Pang, J., Wu, M., Li, J., Zhao, X., & Xia, Y. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2508426 · Cited by 68 · see citing works
Shao, X., Liu, L., Zhou, Y., Zhong, K., Gu, J., Hu, T., Yao, Y., Zhou, C., & Chen, W. (2023) · International Journal of Biological Sciences · doi:10.7150/ijbs.86717 · Cited by 64 · see citing works
Role of bacteriophages in shaping gut microbial community
Mahmud, M. R., Tamanna, S. K., Akter, S., Mazumder, L., Akter, S., Hasan, M. R., Acharjee, M., Esti, I. Z., Islam, M. S., Shihab, M., et al. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2390720 · Cited by 67 · see citing works
The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health
Emencheta, S. C., Olovo, C. V., Eze, O. C., Kalu, C. F., Berebon, D. P., Onuigbo, E. B., Vila, M. M. D. C., Balcão, V. M., & Attama, A. A. (2023) · Pharmaceutics · doi:10.3390/pharmaceutics15102416 · Cited by 68 · see citing works
Phage Therapy as a Novel Therapeutic for the Treatment of Bone and Joint Infections
Suh, G. A., Ferry, T., & Abdel, M. P. (2023) · Clinical Infectious Diseases · doi:10.1093/cid/ciad533 · Cited by 62 · see citing works
Virwani, P. D., Qian, G., Hsu, M. S. S., Pijarnvanit, T. K. K. T. S., Cheung, C. N.-M., Chow, Y. H., Lok Kan, T. A. N. G., Tse, Y.-H., Xian, J.-W., Shirley Sau-Wing, L. A. M., et al. (2023) · Hypertension · doi:10.1161/hypertensionaha.122.20752 · Cited by 61 · see citing works
Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota
Carasso, S., Zaatry, R., Hajjo, H., Kadosh-Kariti, D., Ben-Assa, N., Naddaf, R., Mandelbaum, N., Pressman, S., Chowers, Y., Gefen, T., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.02.003 · Cited by 61 · see citing works
Sun, W., Chen, Y., Wang, L., Wang, Z., Liu, S., Zhang, M., Li, Q., Li, Q., & Zhang, H. (2023) · Biomaterials · doi:10.1016/j.biomaterials.2023.122039 · Cited by 60 · see citing works
Large-scale phage cultivation for commensal human gut bacteria
Shen, J., Zhang, J., Mo, L., Li, Y., Li, Y., Li, C., Kuang, X., Tao, Z., Qu, Z., Wu, L. H., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.03.013 · Cited by 60 · see citing works
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 59 · see citing works
Modelling the Gastrointestinal Carriage of Klebsiella pneumoniae Infections
Calderón-Gonzalez, R., Lee, A., López-Campos, G., Hancock, S. J., Sá-Pessoa, J., Dumigan, A., McMullan, R., Campbell, E. L., & Bengoechea, J. (2022) · bioRxiv · doi:10.1128/mbio.03121-22 · Cited by 53 · see citing works
zhao, M., Li, H., Gan, D., Wang, M., Deng, H., & Yang, Q. (2024) · mSystems · doi:10.1128/msystems.00607-24 · Cited by 57 · see citing works
Emerging clinical relevance of microbiome in cancer: promising biomarkers and therapeutic targets
Dai, J.-H., Tan, X.-R., Qiao, H., & Liu, N. (2023) · Protein & Cell · doi:10.1093/procel/pwad052 · Cited by 56 · see citing works
Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae
Hecht, A. L., Harling, L. C., Friedman, E. S., Tanes, C., Lee, J., Firrman, J., Hao, F., Tu, V., Liu, L., Patterson, A. D., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci174726 · Cited by 57 · see citing works
Borin, J. M., Liu, R., Wang, Y., Wu, T., Chopyk, J., Huang, L., Kuo, P., Ghose, C., Meyer, J. R., Tu, X. M., et al. (2023) · Gut Microbes · doi:10.1080/19490976.2023.2236750 · Cited by 56 · see citing works
The human microbiome in clinical translation: from bench to bedside
Bautista, J., Echeverría, C. E., Maldonado-Noboa, I., Ojeda-Mosquera, S., Hidalgo-Tinoco, C., & López-Cortés, A. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1632435 · Cited by 55 · see citing works
The role of gut microbiome in inflammatory bowel disease diagnosis and prognosis
Zheng, J., Sun, Q., Zhang, J., & Ng, S. C. (2022) · United European Gastroenterology Journal · doi:10.1002/ueg2.12338 · Cited by 54 · see citing works
Tang, N., Ding, Z., Zhang, S., Luo, D., Liu, X., Bao, X., Liu, C., & Liu, Z. (2023) · Advanced Functional Materials · doi:10.1002/adfm.202305133 · Cited by 54 · see citing works
Phage therapy: Targeting intestinal bacterial microbiota for the treatment of liver diseases
Fujiki, J., & Schnabl, B. (2023) · JHEP Reports · doi:10.1016/j.jhepr.2023.100909 · Cited by 57 · see citing works
Precision microbiota therapy for IBD: premise and promise
Nagayama, M., Gogokhia, L., & Longman, R. S. (2025) · Gut microbes · doi:10.1080/19490976.2025.2489067 · Cited by 56 · see citing works
Metabolic network of the gut microbiota in inflammatory bowel disease
Sugihara, K., & Kamada, N. (2024) · Inflammation and Regeneration · doi:10.1186/s41232-024-00321-w · Cited by 54 · see citing works
Contribution of pks+ Escherichia coli (E. coli) to Colon Carcinogenesis
Sadeghi, M., Mestivier, D., & Sobhani, I. (2024) · Microorganisms · doi:10.3390/microorganisms12061111 · Cited by 55 · see citing works
Chen, M., Li, Y., Zhai, Z., Wang, H., Lin, Y., Chang, F., Ge, S., Sun, X., Wei, W., Wang, D., et al. (2025) · Bone Research · doi:10.1038/s41413-024-00381-1 · Cited by 56 · see citing works
Effects of bacteriophages on gut microbiome functionality
Kurilovich, E., & Geva-Zatorsky, N. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2481178 · Cited by 51 · see citing works
Yin, Y., Li, Z., Gao, H., Zhou, D., Zhu, Z., Tao, L., Guan, W.-X., Gao, Y.-F., Song, Y.-J., & Wang, M. (2024) · Nano letters (Print) · doi:10.1021/acs.nanolett.3c03580 · Cited by 49 · see citing works
Turjeman, S. C., Rozera, T., Elinav, E., Ianiro, G., & Koren, O. (2025) · Cell · doi:10.1016/j.cell.2025.01.038 · Cited by 53 · see citing works
Self-citationWeiner, I. N., Kahan-Hanum, M., Buchshtab, N., Zelcbuch, L., Navok, S., Sherman, I., Nicenboim, J., Axelrod, T., Berko-Ashur, D., Olshina, M. A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-60598-4 · Cited by 52 · see citing works
Self-citationPorcari, S., Ng, S. C., Zitvogel, L., Sokol, H., Weersma, R. K., Elinav, E., Gasbarrini, A., Cammarota, G., Tilg, H., & Ianiro, G. (2025) · Cell · doi:10.1016/j.cell.2025.04.016 · Cited by 50 · see citing works
Self-citationMessenger RNA-Based Therapeutics and Vaccines: What’s beyond COVID-19?
Li, D., Liu, C., Li, Y., Tenchov, R., Sasso, J. M., Zhang, D., Li, D., Zou, L., Wang, X., & Zhou, Q. A. (2023) · ACS Pharmacology & Translational Science · doi:10.1021/acsptsci.3c00047 · Cited by 49 · see citing works
Role of the gut microbiota in tumorigenesis and treatment
Liu, Q., Yang, Y., Pan, M., Yang, F., Yu, Y., & Qian, Z. (2024) · Theranostics · doi:10.7150/thno.91700 · Cited by 43 · see citing works
Challenges in IBD Research 2024: Preclinical Human IBD Mechanisms
Ciorba, M. A., Konnikova, L., Hirota, S. A., Lucchetta, E. M., Turner, J. R., Slavin, A., Johnson, K., Condray, C. D., Hong, S., Cressall, B. K., et al. (2024) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izae081 · Cited by 44 · see citing works
Rotman, E. R., McClure, S., Glazier, J., Fuerte-Stone, J., Foldi, J., Erani, A., McGann, R., Arnold, J. H., Lin, H., Valaitis, S. R., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.09.004 · Cited by 45 · see citing works
Krueger, M. E., Boles, J. S., Simon, Z. D., Alvarez, S. D., McFarland, N. R., Okun, M. S., Zimmermann, E. M., Forsmark, C. E., & Tansey, M. G. (2025) · npj Parkinson s Disease · doi:10.1038/s41531-025-00894-4 · Cited by 42 · see citing works
The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome
Su, Q., Lau, R. I., Liu, Q., Li, M. K. T., Mak, J. W. Y., Lu, W., Lau, I. S. F., Lau, L. H. S., Yeung, G. T. Y., Cheung, C. P., et al. (2024) · Cell Host & Microbe · doi:10.1016/j.chom.2024.04.005 · Cited by 41 · see citing works
Shi, J., Zhou, J., Liu, B., Lin, K., Xie, X., Han, X., Sheng, Y., Liu, Y., He, C., Zhou, Y., et al. (2024) · Journal of Nanobiotechnology · doi:10.1186/s12951-024-02725-9 · Cited by 41 · see citing works
Self-citationThe Gut Microbiome Advances Precision Medicine and Diagnostics for Inflammatory Bowel Diseases
Mousa, W. K., & Ali, A. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252011259 · Cited by 44 · see citing works
Gene–environment interactions shape the host–microbial interface in inflammatory bowel disease
Cadwell, K., & Loke, P. (2025) · Nature Immunology · doi:10.1038/s41590-025-02197-5 · Cited by 41 · see citing works
The Role of Dietary Fibers in the Management of IBD Symptoms
Rosa, C. D., Altomare, A., Imperia, E., Spiezia, C., Khazrai, Y. M., & Guarino, M. P. L. (2022) · Nutrients · doi:10.3390/nu14224775 · Cited by 40 · see citing works
Porcari, S., Fusco, W. G., Spivak, I., Fiorani, M., Gasbarrini, A., Elinav, E., Cammarota, G., & Ianiro, G. (2024) · The Lancet. Gastroenterology & hepatology · doi:10.1016/s2468-1253(23)00357-6 · Cited by 42 · see citing works
Self-citationZhu, J., Chen, T., Ju, Y., Dai, J., & Zhuge, X. (2024) · Pharmaceuticals · doi:10.3390/ph17091206 · Cited by 40 · see citing works
Jiang, J., Ma, Y., Zhou, L., Han, W., Liang, Y., Dong, J., Ding, Y., Li, W., Qi, L., Li, J., et al. (2025) · Advanced Materials · doi:10.1002/adma.202417050 · Cited by 40 · see citing works
Microbiome Dysbiosis: A Pathological Mechanism at the Intersection of Obesity and Glaucoma
Pezzino, S., Sofia, M., Greco, L. P., Litrico, G., Filippello, G., Sarvà, I., Greca, G. L., & Latteri, S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24021166 · Cited by 39 · see citing works
Bacteriophage defends murine gut from Escherichia coli invasion via mucosal adherence
Wu, J., Fu, K., Hou, C., Wang, Y., Ji, C., Xue, F., Ren, J., Dai, J., Barr, J. J., & Tang, F. (2024) · Nature Communications · doi:10.1038/s41467-024-48560-2 · Cited by 38 · see citing works
Hong, D., Zhang, C., Wu, W., Lu, X., & Zhang, L. (2023) · Frontiers in Neurology · doi:10.3389/fneur.2023.1133546 · Cited by 38 · see citing works
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Asokan, S., Cullin, N., Stein‐Thoeringer, C. K., & Elinav, E. (2023) · Cancers · doi:10.3390/cancers15030794 · Cited by 39 · see citing works
Self-citationStructure-guided discovery of anti-CRISPR and anti-phage defense proteins
Duan, N., Hand, E., Pheko, M., Sharma, S., & Emiola, A. (2024) · Nature Communications · doi:10.1038/s41467-024-45068-7 · Cited by 38 · see citing works
Tian, X., Li, S., Wang, C., Zhang, Y., Feng, X., Yan, Q., Guo, R., Wu, F., Wu, C., Wang, Y., et al. (2024) · Microbiome · doi:10.1186/s40168-024-01832-x · Cited by 39 · see citing works
The potential use of bacteriophages as antibacterial agents against Klebsiella pneumoniae
Gholizadeh, O., Ghaleh, H. E. G., Tat, M., Ranjbar, R., & Dorostkar, R. (2024) · Virology Journal · doi:10.1186/s12985-024-02450-7 · Cited by 38 · see citing works
Ameba-inspired strategy enhances probiotic efficacy via prebound nutrient supply
Pan, C., Jiang, X., Wei, J., Liu, C., Zhang, M., Gao, C., Chen, R., Yang, C., Wang, B., Yu, M., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57071-7 · Cited by 44 · see citing works
Diet-microbiome interactions in cancer
Abdeen, S. K., Mastandrea, I., Stinchcombe, N., Puschhof, J., & Elinav, E. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.03.013 · Cited by 36 · see citing works
Self-citationBacteriophage-mediated manipulations of microbiota in gastrointestinal diseases
Haddad, L. E., Mendoza, J. F., & Jobin, C. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1055427 · Cited by 40 · see citing works
Yu, F., Hu, X., Ren, H., Wang, X., Shi, R., Guo, J., Chang, J., Zhou, X., Jin, Y., Li, Y., et al. (2024) · Journal of Translational Medicine · doi:10.1186/s12967-024-05026-9 · Cited by 37 · see citing works
Wu, X., Wei, J., Wang, R., Liu, D., Yi, Y., Gong, M., Liu, X., Gong, Q., Li, H., & Gao, J.-M. (2025) · Advanced Science · doi:10.1002/advs.202412234 · Cited by 37 · see citing works
Microbiota-mediated mechanisms of mucosal immunity across the lifespan
Iliev, I. D., Blander, J. M., Collins, N., Guo, C., Longman, R., Sonnenberg, G. F., Zeng, M. Y., & Artis, D. (2025) · Nature Immunology · doi:10.1038/s41590-025-02281-w · Cited by 43 · see citing works
- Authors
- Federici, S., Kredo-Russo, S., Valdés-Mas, R., Kviatcovsky, D., Weinstock, E., Matiuhin, Y., Silberberg, Y., Atarashi, K., Furuichi, M., Oka, A., Liu, B., Fibelman, M., Weiner, I. N., Khabra, E., Cullin, N., Ben-Yishai, N., Inbar, D., Ben-David, H., Nicenboim, J., Kowalsman, N., Lieb, W., Kario, E., Cohen, T., Geffen, Y. F., Zelcbuch, L., Cohen, A., Rappo, U., Gahali-Sass, I., Golembo, M., Lev, V., Dori-Bachash, M., Shapiro, H., Moresi, C., Cuevas-Sierra, A., Mohapatra, G., Kern, L., Zheng, D., Nobs, S. P., Suez, J., Stettner, N., Harmelin, A., Zak, N., Puttagunta, S., Bassan, M., Honda, K., Sokol, H., Bang, C., Franke, A., Schramm, C., Maharshak, N., Sartor, R. B., Sorek, R., & Elinav, E.
- Affiliations
- Weizmann Institute of Science (IL)
- Keio University (JP)
- University of North Carolina at Chapel Hill (US)
- Tel Aviv University (IL)
- German Cancer Research Center (DE)
- Christian-Albrechts-Universität zu Kiel (DE)
- Inserm (FR)
- University Medical Center Hamburg-Eppendorf (DE)
- Corresponding author
- Elinav, Eran
- ORCID
- Federici, Sara
- Kviatcovsky, Denise
- Matiuhin, Yulia
- Atarashi, Koji
- Furuichi, Munehiro
- Oka, Akihiko
- Liu, Bo
- Weiner, Iddo Nadav
- Cullin, Nyssa
- Lieb, Wolfgang
- Cohen, Tal
- Rappo, Urania
- Shapiro, Hagit
- Moresi, Claudia
- Kern, Lara
- Zheng, Danping
- Nobs, Samuel Philip
- Suez, Jotham
- Stettner, Noa
- Harmelin, Alon
- Honda, Kenya
- Sokol, Harry
- Bang, Corinna
- Schramm, Christoph
- Maharshak, Nitsan
- Sartor, Ryan Balfour
- Sorek, Rotem
- Elinav, Eran
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2022-08
- Volume
- 185
- Issue
- 16
- Pages
- 2879-2898.e24
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W4289780574
- Cited by
- 542
- References
- 121
- Citations by year
- 2026: 124 · 2025: 152 · 2024: 130 · 2023: 108 · 2022: 27
- FWCI
- 56.34
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 368 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion, other-oa)
- HAL (submittedVersion)
- Funders
- Japan Society for the Promotion of Science (20H05627)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Keywords
- inflammatory bowel disease, Klebsiella pneumoniae, phage therapy, bacteriophages, gut commensals, intestinal inflammation, antibiotic resistance, mobilome, colitis, germ-free mice, gastric acid, pathobionts, disease severity
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteriophages, Colitis, Humans, Inflammation, Klebsiella pneumoniae, Inflammatory Bowel Diseases, Mice
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