Cited by 546Bacteriophages and microbial interactionsGut microbiota and healthInflammatory Bowel Disease

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Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

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Federici, Sara, Kredo-Russo, Sharon, Valdés-Mas, Rafael, Kviatcovsky, Denise, Weinstock, Eyal, Matiuhin, Yulia, Silberberg, Yael, Atarashi, Koji, Furuichi, Munehiro, Oka, Akihiko, Liu, Bo, Fibelman, Morine, Weiner, Iddo Nadav, Khabra, Efrat, Cullin, Nyssa, Ben-Yishai, Noa, Inbar, Dana, Ben-David, Hava, Nicenboim, Julian, Kowalsman, Noga, Lieb, Wolfgang, Kario, Edith, Cohen, Tal, Geffen, Yael Friedman, Zelcbuch, Lior, Cohen, Ariel, Rappo, Urania, Gahali-Sass, Inbar, Golembo, Myriam, Lev, Vered, Dori-Bachash, Mally, Shapiro, Hagit, Moresi, Claudia, Cuevas-Sierra, Amanda, Mohapatra, Gayatree, Kern, Lara, Zheng, Danping, Nobs, Samuel Philip, Suez, Jotham, Stettner, Noa, Harmelin, Alon, Zak, Naomi, Puttagunta, Sailaja, Bassan, Merav, Honda, Kenya, Sokol, Harry, Bang, Corinna, Franke, Andre, Schramm, Christoph, Maharshak, Nitsan, Sartor, Ryan Balfour, Sorek, Rotem, Elinav, Eran·2022·Cell

DOI 10.1016/j.cell.2022.07.003

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Abstract

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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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
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
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty560 · Cited by 29,721
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 26,206
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
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
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 5,947
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
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

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Sabouri Ghannad, 2012, Bacteriophage: time to re-evaluate the potential of phage therapy as a promising agent to control multidrug-resistant bacteria, Iran. J. Basic Med. Sci., 15, 693

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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 59
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Yin, Y. B., Li, Z., Gao, H., Zhou, D., Zhu, Z., Tao, L., Guan, W., Gao, Y., Song, Y., & Wang, M. (2024) · Nano Letters · doi:10.1021/acs.nanolett.3c03580 · Cited by 53
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Turjeman, S., Rozera, T., Elinav, E., Ianiro, G., & Koren, O. (2025) · Cell · doi:10.1016/j.cell.2025.01.038 · Cited by 58
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Weiner, 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 63
Self-citation
The microbiome for clinicians
Porcari, 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 56
Self-citation
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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 46
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
Rapid design of bacteriophage cocktails to suppress the burden and virulence of gut-resident carbapenem-resistant Klebsiella pneumoniae
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 48
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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
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Zhu, J., Chen, T., Ju, Y., Dai, J., & Zhuge, X. (2024) · Pharmaceuticals · doi:10.3390/ph17091206 · Cited by 45
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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
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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
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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
The Gut Microbiota‐Xanthurenic Acid‐Aromatic Hydrocarbon Receptor Axis Mediates the Anticolitic Effects of Trilobatin
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
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 48

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)
DOI: 10.1016/j.cell.2022.07.003
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: Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Gastroenterology › 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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Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

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