Dynamic modulation of the gut microbiota and metabolome by bacteriophages in a mouse model
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Abstract
The human gut microbiome is comprised of densely colonizing microorganisms including bacteriophages, which are in dynamic interaction with each other and the mammalian host. To address how bacteriophages impact bacterial communities in the gut, we investigated the dynamic effects of phages on a model microbiome. Gnotobiotic mice were colonized with defined human gut commensal bacteria and subjected to predation by cognate lytic phages. We found that phage predation not only directly impacts susceptible bacteria but also leads to cascading effects on other bacterial species via interbacterial interactions. Metabolomic profiling revealed that shifts in the microbiome caused by phage predation have a direct consequence on the gut metabolome. Our work provides insight into the ecological importance of phages as modulators of bacterial colonization, and it additionally suggests the potential impact of gut phages on the mammalian host with implications for their therapeutic use to precisely modulate the microbiome.
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Phages reshape tumor-associated bacterial communities.
“Indirectly, phages reshape tumor-associated bacterial communities, depleting protumorigenic taxa and altering microbial metabolites that regulate inflammation, genotoxic stress, and therapeutic response [20–23]”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Introduction and Discussion describe phages reshaping a defined community of commensal gut bacteria in gnotobiotic mice. They do not establish that the community was tumor-associated, so the claim extends the finding to a setting this study did not examine. No page numbers were provided for these passages. (LLM, conf=0.88)
Experimental — accuracy not yet measuredPhages deplete protumorigenic taxa.
“Indirectly, phages reshape tumor-associated bacterial communities, depleting protumorigenic taxa and altering microbial metabolites that regulate inflammation, genotoxic stress, and therapeutic response [20–23]”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Results section reports that phages knocked down targeted gut bacteria and indirectly reduced B. fragilis in a defined mouse microbiota. It does not identify those bacteria as protumorigenic or study tumor-associated communities, so the cancer-specific part of the claim is unsupported. (LLM, conf=0.87)
Experimental — accuracy not yet measuredPhages can eliminate cancer-associated bacteria.
“Phages can eliminate cancer-associated bacteria, remodel the tumor microenvironment, enhance antitumor immunity, and deliver targeted therapeutic payloads.”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Results report that phages lysed susceptible gut bacteria and reduced their numbers in mice. But the Discussion explicitly says the targeted bacteria experienced “knockdown but not eradication,” and the paper does not study cancer-associated bacteria. It therefore supports bacterial targeting, not the claimed elimination in a cancer context. (LLM, conf=0.87)
Experimental — accuracy not yet measuredPhages alter microbial metabolites that regulate inflammation, genotoxic stress, and therapeutic response.
“Indirectly, phages reshape tumor-associated bacterial communities, depleting protumorigenic taxa and altering microbial metabolites that regulate inflammation, genotoxic stress, and therapeutic response [20–23]”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Introduction and Results (‘Bacterial Modulation Induced by Phages Impacts the Gut Metabolome’; page unavailable) report that phages shifted gut bacterial populations and fecal metabolites in mice. The paper does not establish that these changes occurred in tumor-associated communities or depleted protumorigenic taxa, nor that the altered metabolites regulated inflammation, genotoxic stress, or therapeutic response. (LLM, conf=0.88)
Experimental — accuracy not yet measuredPhages enable highly selective removal of cancer-associated bacteria within the gut or tumor niche, avoiding broad collateral damage to commensal communities associated with conventional antibiotics.
“In parallel, phages enable highly selective removal of cancer-associated bacteria within the gut or tumor niche (Table 1), avoiding the broad collateral damage to commensal communities associated with conventional antibiotics [15,17,20,62,63]”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Results (page not available) show that the phages selectively lysed their susceptible gut bacteria in a defined mouse community. The paper does not study cancer-associated bacteria or a tumor niche, nor does it compare phages with antibiotics. Its Introduction also reports changes in non-targeted commensals, so avoidance of collateral effects is overstated. (LLM, conf=0.88)
Experimental — accuracy not yet measured
Gnotobiotic systems allow precise control of microbial composition, enabling dissection of how specific bacteria influence phage pharmacokinetics, biodistribution, and therapeutic efficacy.
“These systems allow precise control of microbial composition, enabling the dissection of how specific bacteria influence phage pharmacokinetics, biodistribution, and therapeutic efficacy.”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Introduction and Discussion describe gnotobiotic mice colonized with a defined bacterial consortium, which allowed the authors to distinguish direct phage targeting from effects mediated by other bacteria. The Results track phage persistence in the gut, but the paper does not establish how specific bacteria affect phage biodistribution or therapeutic efficacy; it discusses therapy only as a potential application. No page numbers were available in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measuredGnotobiotic mice provide unparalleled mechanistic insight into phage-bacteria-host immunity interactions.
“Given the interplay between phages, bacteria, and host immunity, gnotobiotic mice provide unparalleled mechanistic insight [20,118]”
From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [20]
The Introduction describes gnotobiotic mice as an attractive model for characterizing phage behavior in the gut, and the Discussion says the defined model helps provide mechanistic insight. But the paper investigates phage–bacteria interactions and gut metabolites, not host immunity; it also calls the model a compromise rather than establishing that its insight is unparalleled. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPhages can cause immune disorders by recognizing foreign genetic elements and destroying their DNA fragments.
“Phages can cause immune disorders by recognizing foreign genetic elements and destroying their DNA fragments (75).”
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 [75]
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Cites
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548 · see citing works
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
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 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.01043-13 · Cited by 7,004 · see citing works
Diversity, stability and resilience of the human gut microbiota
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012) · Nature · doi:10.1038/nature11550 · Cited by 5,533 · see citing works
Revised Estimates for the Number of Human and Bacteria Cells in the Body
Sender, R., Fuchs, S., & Milo, R. (2016) · PLOS Biology · doi:10.1371/journal.pbio.1002533 · Cited by 5,425 · see citing works
Role of the microbiota in immunity and inflammation.
Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385 · see citing works
Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works
Trophic Downgrading of Planet Earth
Estes, J. A., Terborgh, J., Brashares, J. S., Power, M. E., Berger, J., Bond, W. J., Carpenter, S. R., Essington, T. E., Holt, R. D., Jackson, J. B. C., et al. (2011) · Science · doi:10.1126/science.1205106 · Cited by 4,087 · cited 1× · see citing works
“Analogous to the importance of understanding apex predators in macroscopic environments (Estes et al., 2011), elucidating the predation behavior of phages has the potential to provide similar insights in the gastrointestinal ecosystem.”
BackgroundThe Human Intestinal Microbiome in Health and Disease
Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637 · see citing works
Caspi, R., Billington, R., Ferrer, L., Foerster, H., Fulcher, C. A., Keseler, I. M., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1164 · Cited by 3,395 · see citing works
Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.024 · Cited by 3,283 · see citing works
Microbiome Datasets Are Compositional: And This Is Not Optional
Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V., & Egozcue, J. J. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02224 · Cited by 3,044 · cited 1× · see citing works
“, 2013), but their use of an uncharacterizedmixture of phage inoculum, inability to verify phage infectivity among the bacterial consortia in vitro, and use of relative abundance not absolute concentrations (Gloor et al., 2017) to longitudinally track the gut bacteria makes it challenging to address questions about di…”
BackgroundBacterial competition: surviving and thriving in the microbial jungle
Hibbing, M. E., Fuqua, C., Parsek, M. R., & Peterson, S. B. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2259 · Cited by 2,658 · see citing works
A Historical Overview of Natural Products in Drug Discovery
Dias, D. A., Urban, S., & Roessner, U. (2012) · Metabolites · doi:10.3390/metabo2020303 · Cited by 2,008 · see citing works
Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk
Zhu, W., Gregory, J. C., Org, E., Buffa, J. A., Gupta, N., Wang, Z., Li, L., Fu, X., Wu, Y., Mehrabian, M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.02.011 · Cited by 1,968 · see citing works
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872 · 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
Persistent gut microbiota immaturity in malnourished Bangladeshi children
Subramanian, S., Huq, S., Yatsunenko, T., Haque, R., Mahfuz, M., Alam, M. A., Benezra, A., DeStefano, J., Meier, M. F., Muegge, B. D., et al. (2014) · Nature · doi:10.1038/nature13421 · Cited by 1,270 · see citing works
Stability criteria for complex ecosystems
Allesina, S., & Tang, S. (2012) · Nature · doi:10.1038/nature10832 · Cited by 1,232 · 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
Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor
Smith, M. I., Yatsunenko, T., Manary, M. J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A. L., Rich, S. S., Concannon, P., Mychaleckyj, J. C., et al. (2013) · Science · doi:10.1126/science.1229000 · Cited by 1,173 · see citing works
Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., & Schmidt, T. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1201 · Cited by 1,118 · see citing works
Yassour, M., Vatanen, T., Siljander, H., Hämäläinen, A.-M., Härkönen, T., Ryhänen, S. J., Franzosa, E. A., Vlamakis, H., Huttenhower, C., Gevers, D., et al. (2016) · Science Translational Medicine · doi:10.1126/scitranslmed.aad0917 · Cited by 1,043 · see citing works
Chang, J. Y., Antonopoulos, D. A., Kalra, A., Tonelli, A., Khalife, W. T., Schmidt, T. M., & Young, V. B. (2008) · The Journal of Infectious Diseases · doi:10.1086/525047 · Cited by 1,010 · see citing works
Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice
Le Roy, T., Llopis, M., Lepage, P., Bruneau, A., Rabot, S., Bevilacqua, C., Martin, P., Philippe, C., Walker, F., Bado, A., et al. (2013) · Gut · doi:10.1136/gutjnl-2012-303816 · Cited by 1,001 · see citing works
Theriot, C. M., Koenigsknecht, M. J., Carlson, P. E., Hatton, G. E., Nelson, A. M., Li, B., Huffnagle, G. B., Z. Li, J., & Young, V. B. (2014) · Nature Communications · doi:10.1038/ncomms4114 · Cited by 974 · see citing works
Commensal bacteria at the interface of host metabolism and the immune system
Brestoff, J. R., & Artis, D. (2013) · Nature Immunology · doi:10.1038/ni.2640 · Cited by 945 · 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
Koskella, B. L., & Brockhurst, M. A. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12072 · Cited by 894 · see citing works
The Human Gut Microbiome: From Association to Modulation
Schmidt, T. S. B., Raes, J., & Bork, P. (2018) · Cell · doi:10.1016/j.cell.2018.02.044 · Cited by 845 · see citing works
Miller, E. S., Kutter, E. M., Mosig, G., Arisaka, F., Kunisawa, T., & Rüger, W. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.1.86-156.2003 · Cited by 828 · see citing works
Bisgaard, H., Li, N., Bonnelykke, K., Chawes, B. L. K., Skov, T., Paludan-Müller, G., Stokholm, J., Smith, B., & Krogfelt, K. A. (2011) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2011.04.060 · Cited by 786 · 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
Low gut microbiota diversity in early infancy precedes asthma at school age
Abrahamsson, T. R., Jakobsson, H. E., Andersson, A. F., Björkstén, B., Engstrand, L., & Jenmalm, M. C. (2014) · Clinical & Experimental Allergy · doi:10.1111/cea.12253 · Cited by 750 · see citing works
Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M. J., Trehan, I., Jorgensen, J. M., et al. (2016) · Science · doi:10.1126/science.aad3311 · Cited by 735 · see citing works
Williams, B. B., Van Benschoten, A. H., Cimermancic, P., Donia, M. S., Zimmermann, M., Taketani, M., Ishihara, A., Kashyap, P. C., Fraser, J. S., & Fischbach, M. A. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.09.001 · Cited by 732 · see citing works
Bacterial colonization factors control specificity and stability of the gut microbiota
Lee, S. M., Donaldson, G. P., Mikulski, Z., Boyajian, S., Ley, K. F., & Mazmanian, S. K. (2013) · Nature · doi:10.1038/nature12447 · Cited by 629 · see citing works
Phage Host Range and Efficiency of Plating
Kutter, E. M. (2009) · Methods in molecular biology · doi:10.1007/978-1-60327-164-6_14 · Cited by 560 · see citing works
Mucin-bacterial interactions in the human oral cavity and digestive tract
Derrien, M., van Passel, M. W. J., van de Bovenkamp, J. H. B., Schipper, R., de Vos, W., & Dekker, J. (2010) · Gut Microbes · doi:10.4161/gmic.1.4.12778 · Cited by 556 · see citing works
Ajslev, T. A., Andersen, C. S., Gamborg, M., Sørensen, T. I. A., & Jess, T. (2011) · International Journal of Obesity · doi:10.1038/ijo.2011.27 · Cited by 534 · see citing works
Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome
Gibson, M. K., Wang, B., Ahmadi, S., Burnham, C.-A. D., Tarr, P. I., Warner, B. B., & Dantas, G. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.24 · Cited by 457 · see citing works
Bhattarai, Y., Williams, B. B., Battaglioli, E. J., Whitaker, W. R., Till, L., Grover, M., Linden, D. R., Akiba, Y., Kandimalla, K. K., Zachos, N. C., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.05.004 · Cited by 436 · 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
Evans, A. M. (2014) · Journal of Postgenomics Drug & Biomarker Development · doi:10.4172/2153-0769.1000132 · Cited by 387 · 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
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
Finding the Missing Links among Metabolites, Microbes, and the Host
Dorrestein, P. C., Mazmanian, S. K., & Knight, R. (2014) · Immunity · doi:10.1016/j.immuni.2014.05.015 · Cited by 317 · see citing works
Effect of Antibiotic Treatment on the Intestinal Metabolome
Antunes, L. C. M., Han, J., Ferreira, R. B. R., Lolić, P., Borchers, C. H., & Finlay, B. B. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01664-10 · Cited by 271 · see citing works
MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses
Bucci, V., Tzen, B., Li, N., Simmons, M., Tanoue, T., Bogart, E., Deng, L., Yeliseyev, V., Delaney, M. L., Liu, Q., et al. (2016) · Genome biology · doi:10.1186/s13059-016-0980-6 · Cited by 253 · see citing works
Self-citationMicrobiome: Focus on Causation and Mechanism
Fischbach, M. A. (2018) · Cell · doi:10.1016/j.cell.2018.07.038 · Cited by 248 · see citing works
Chibani-Chennoufi, S., Sidoti, J., Bruttin, A., et al. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.7.2558-2569.2004 · Cited by 234 · see citing works
Tyramine and Phenylethylamine Biosynthesis by Food Bacteria
Marcobal, A. M., Rivas, B. D. L., Landete, J. M., Tabera, L., & Múñoz, R. (2012) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2010.500545 · Cited by 197 · see citing works
Bacteriophages active against Bacteroides fragilis in sewage-polluted waters
Tartera, C., & Jofre, J. (1987) · Applied and Environmental Microbiology · doi:10.1128/aem.53.7.1632-1637.1987 · Cited by 196 · see citing works
Evolutionary consequences of intra-patient phage predation on microbial populations
Seed, K. D., Yen, M., Shapiro, B. J., et al. (2014) · eLife · doi:10.7554/elife.03497 · Cited by 145 · see citing works
Galtier, M., Sordi, L. D., Maura, D., Arachchi, H., Volant, S., Dillies, M., & Debarbieux, L. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13284 · Cited by 142 · see citing works
Connil, N., Breton, Y. S. L., Dousset, X., Auffray, Y., Rincé, A., & Prévost, H. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.7.3537-3544.2002 · Cited by 134 · see citing works
The costs of evolving resistance in heterogeneous parasite environments
Koskella, B. L., Lin, D. M., Buckling, A. G. J., & Thompson, J. N. (2011) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2011.2259 · Cited by 126 · see citing works
In vivo replication of T4 and T7 bacteriophages in germ-free mice colonized with Escherichia coli
Weiss, M., Denou, E., Bruttin, A., Serra-Moreno, R., Dillmann, M.-L., & Brüssow, H. (2009) · Virology · doi:10.1016/j.virol.2009.07.020 · Cited by 113 · see citing works
T4 phages against Escherichia coli diarrhea: Potential and problems
Denou, E., Bruttin, A., Barretto, C., et al. (2009) · Virology · doi:10.1016/j.virol.2009.03.009 · Cited by 109 · see citing works
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 · see citing works
Maura, D., Morello, E., du Merle, L., Bomme, P., Bouguénec, C. L., & Debarbieux, L. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02644.x · Cited by 99 · see citing works
Impact of Phages on Two-Species Bacterial Communities
Harcombe, W. R., & Bull, J. J. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.9.5254-5259.2005 · Cited by 99 · see citing works
Effect of Phage on the Infectivity of Vibrio cholerae and Emergence of Genetic Variants
Zahid, M. S. H., Udden, S. M. N., Faruque, A. S. G., et al. (2008) · Infection and Immunity · doi:10.1128/iai.00578-08 · Cited by 76 · see citing works
Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems
Gerber, G. K., Onderdonk, A. B., & Bry, L. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002624 · Cited by 65 · see citing works
Self-citationISOLATION AND CHARACTERIZATION OF BACTERIOPHAGES ACTIVE ON CLOSTRIDIUM SPOROGENES
Betz, J. V., & Anderson, K. E. (1964) · Journal of Bacteriology · doi:10.1128/jb.87.2.408-415.1964 · Cited by 29 · see citing works
A large new Streptococcus bacteriophage
Ackermann, H.-W., Caprioli, T., & Kasatiya, S. S. (1975) · Canadian Journal of Microbiology · doi:10.1139/m75-080 · Cited by 22 · see citing works
Albright, M., Chase, A. B., Martiny, J. B. H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.122 · Cited by 7 · see citing works
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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
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Maternal vertical transmission affecting early-life microbiota development
Wang, S., Ryan, C. A., Boyaval, P., Dempsey, E. M., Ross, R. P., & Stanton, C. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2019.07.010 · Cited by 243 · 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
Sharpton, S. R., Schnabl, B., Knight, R., & Loomba, R. (2021) · Cell Metabolism · doi:10.1016/j.cmet.2020.11.010 · Cited by 194 · see citing works
Vemuri, R., Shankar, E. M., Chieppa, M., Eri, R., & Kavanagh, K. (2020) · Microorganisms · doi:10.3390/microorganisms8040483 · Cited by 162 · see citing works
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Shuwen, H., & Kefeng, D. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2113717 · Cited by 124 · see citing works
Targeting the human gut microbiome with small-molecule inhibitors
Woo, A. Y. M., Aguilar Ramos, M. A., Narayan, R., Richards-Corke, K. C., Wang, M. L., Sandoval-Espinola, W. J., & Balskus, E. P. (2023) · Nature Reviews Chemistry · doi:10.1038/s41570-023-00471-4 · Cited by 42 · 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
Phage therapy in oncology: opportunities for cancer prevention and treatment
Mutalik, V. K., Inman, J. L., Chang, H., Arkin, A., & Mao, J.-H. (2026) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2026.02.001 · Cited by 5 · see citing works
- Authors
- Hsu, B. B., Gibson, T. E., Yeliseyev, V., Liu, Q., Lyon, L., Bry, L., Silver, P. A., & Gerber, G. K.
- Affiliations
- Harvard University (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Silver, Pamela A.
- Gerber, Georg K.
- ORCID
- Venue
- Cell Host & Microbe
- Publisher
- Elsevier BV
- Published
- 2019-06
- Volume
- 25
- Issue
- 6
- Pages
- 803-814.e5
- ISSN
- 1931-3128 (ISSN-L)
- PMC
- PMC6579560
- OpenAlex
- W2948347995
- Cited by
- 573
- References
- 69
- Citations by year
- 2026: 89 · 2025: 83 · 2024: 71 · 2023: 76 · 2022: 80 · 2021: 95 · 2020: 57 · 2019: 22
- FWCI
- 41.13
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell Host & Microbe (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Bill & Melinda Gates Foundation (OPP1150555)
- DARPA (BRICS HR0011-15-C-0094)
- NIH (T32 HL007627)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- bacteriophages, gut microbiota, phage predation, lytic phages, gnotobiotic mice, interbacterial interactions, gut metabolome, metabolite profiling, phage therapy, host-microbe interactions
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteriolysis, Bacteriophages, Feces, Germ-Free Life, Mice, Metabolome, Microbial Interactions
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