Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae
Open accessAbstract
Infections by multidrug-resistant Enterobacteriaceae(MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization.Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Administration of Lactobacillus to antibiotic-treated mice increased faecal butyrate levels and decreased intestinal colonization by Klebsiella pneumoniae.
“Administration of Lactobacillus to antibiotic-treated mice increased faecal butyrate levels and decreased intestinal colonization by Klebsiella pneumoniae [38].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [38]
Lactobacillus species promote an overall increase in microbiota density following antibiotic treatment in mice.
“Another study, by Djukovic and colleagues, established that Lactobacillus species promoted the recovery of Eubacteriales and an overall increase in microbiota density following antibiotic treatment in mice [38].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [38]
Butyrate is inhibitory to multidrug-resistant Enterobacteriaceae.
“The increase in Eubacteriales was associated with an increase of SCFA, notably butyrate, which was inhibitory to multidrug-resistant Enterobacteriaceae.”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [38]
The increase in Eubacteriales following antibiotic treatment is associated with an increase of SCFA, notably butyrate.
“The increase in Eubacteriales was associated with an increase of SCFA, notably butyrate, which was inhibitory to multidrug-resistant Enterobacteriaceae.”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [38]
Lactobacillus species promote recovery of Eubacteriales following antibiotic treatment in mice.
“Another study, by Djukovic and colleagues, established that Lactobacillus species promoted the recovery of Eubacteriales and an overall increase in microbiota density following antibiotic treatment in mice [38].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [38]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · 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
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889 · 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
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · see citing works
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 19,770 · see citing works
Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192 · see citing works
UCHIME improves sensitivity and speed of chimera detection
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114 · see citing works
KEGG as a reference resource for gene and protein annotation
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1070 · Cited by 7,387 · see citing works
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682 · see citing works
Tacconelli, E., Carrara, E., Savoldi, A., Harbarth, S., Mendelson, M., Monnet, D. L., Pulcini, C., Kahlmeter, G., Kluytmans, J., Carmeli, Y., et al. (2018) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(17)30753-3 · Cited by 6,142 · see citing works
HMMER web server: interactive sequence similarity searching
Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952 · see citing works
Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313 · see citing works
The neuroactive potential of the human gut microbiota in quality of life and depression
Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0337-x · Cited by 1,963 · 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
Self-citationIroning out the wrinkles in the rare biosphere through improved OTU clustering
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02193.x · Cited by 1,346 · see citing works
Wang, Y., & Qian, P. (2009) · PLoS ONE · doi:10.1371/journal.pone.0007401 · Cited by 1,270 · see citing works
Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion
Byndloss, M. X., Olsan, E. E., Rivera-Chávez, F., Tiffany, C. R., Cevallos, S. A., Lokken, K. L., Torres, T. P., Byndloss, A. J., Faber, F., Gao, Y., et al. (2017) · Science · doi:10.1126/science.aam9949 · Cited by 1,236 · see citing works
Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.047 · Cited by 1,184 · see citing works
Duncan, S. H., Louis, P., & Flint, H. J. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.10.5810-5817.2004 · Cited by 1,124 · see citing works
Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., Viale, A., Socci, N. D., van den Brink, M. R. M., Kamboj, M., et al. (2010) · Journal of Clinical Investigation · doi:10.1172/jci43918 · Cited by 943 · see citing works
Colonization resistance of the digestive tract in conventional and antibiotic-treated mice
van der Waaij, D., Vries, J. M. B.-D., & der Wees, J. E. C. L.-V. (1971) · Journal of Hygiene · doi:10.1017/s0022172400021653 · Cited by 907 · see citing works
Rivera-Chávez, F., Zhang, L. F., Faber, F., Lopez, C. A., Byndloss, M. X., Olsan, E. E., Xu, G., Velazquez, E. M., Lebrilla, C. B., Winter, S. E., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.03.004 · Cited by 864 · see citing works
MetaboLights: a resource evolving in response to the needs of its scientific community
Haug, K., Cochrane, K., Nainala, V. C., Williams, M., Chang, J., Jayaseelan, K. V., & O’Donovan, C. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1019 · Cited by 694 · see citing works
Donskey, C. J., Chowdhry, T. K., Hecker, M. T., Hoyen, C. K., Hanrahan, J., Hujer, A. M., Hutton‐Thomas, R., Whalen, C. C., Bonomo, R. A., & Rice, L. B. (2000) · New England Journal of Medicine · doi:10.1056/nejm200012283432604 · Cited by 691 · see citing works
Buffie, C. G., Jarchum, I., Equinda, M., Lipuma, L., Gobourne, A., Viale, A., Ubeda, C., Xavier, J., & Pamer, E. G. (2012) · Infection and Immunity · doi:10.1128/iai.05496-11 · Cited by 596 · cited 1× · see citing works
“Weused 6different kmer lengths (21, 33, 55, 77, 99, 127), as it is the best kmer combination for estimated read sizes over 250bp.”
MethodSelf-citationWalter, J., Armet, A. M., Finlay, B. B., & Shanahan, F. (2020) · Cell · doi:10.1016/j.cell.2019.12.025 · Cited by 596 · see citing works
Gorrie, C. L., Mirčeta, M., Wick, R. R., Edwards, D., Thomson, N. R., Strugnell, R. A., Pratt, N. F., Garlick, J. S., Watson, K., Pilcher, D. V., et al. (2017) · Clinical Infectious Diseases · doi:10.1093/cid/cix270 · Cited by 581 · see citing works
Microcins mediate competition among Enterobacteriaceae in the inflamed gut
Sassone-Corsi, M., Nuccio, S.-P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raffatellu, M. (2016) · Nature · doi:10.1038/nature20557 · Cited by 549 · see citing works
Canani, R. B., Sangwan, N., Stefka, A. T., Nocerino, R., Paparo, L., Aitoro, R., Calignano, A., Khan, A. A., Gilbert, J. A., & Nagler‐Anderson, C. (2015) · The ISME Journal · doi:10.1038/ismej.2015.151 · Cited by 525 · see citing works
A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection
Jacobson, A., Lam, L., Rajendram, M., Tamburini, F., Honeycutt, J., Pham, T., Van Treuren, W., Pruss, K., Stabler, S. R., Lugo, K., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.07.002 · Cited by 507 · see citing works
Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Vital, M., Karch, A., & Pieper, D. H. (2017) · mSystems · doi:10.1128/msystems.00130-17 · Cited by 487 · see citing works
Short- and long-term effects of oral vancomycin on the human intestinal microbiota
Isaac, S., Scher, J. U., Djuković, A., Jiménez‐Hernández, N., Littman, D. R., Abramson, S. B., Pamer, E. G., & Úbeda, C. (2016) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkw383 · Cited by 320 · see citing works
Analysis of Microbiome Data in the Presence of Excess Zeros
Kaul, A., Mandal, S., Davidov, O., & Peddada, S. D. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02114 · Cited by 320 · see citing works
Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium
Caballero, S., Kim, S., Carter, R. A., Leiner, I. M., Sušac, B., Miller, L., Kim, G. J., Ling, L., & Pamer, E. G. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.04.002 · Cited by 308 · see citing works
Maltby, R., Leatham-Jensen, M. P., Gibson, T., Cohen, P. S., & Conway, T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053957 · Cited by 285 · see citing works
The Genomic Diversification of the Whole Acinetobacter Genus: Origins, Mechanisms, and Consequences
Touchon, M., Cury, J., Yoon, E.-J., Křížová, L., Cerqueira, G., Murphy, C. I., Feldgarden, M., Wortman, J. R., Clermont, D., Lambert, T., et al. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu225 · Cited by 273 · see citing works
Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens
Kim, Y., Sakamoto, K., Seo, S., Pickard, J. M., Gillilland, M. G., Pudlo, N. A., Hoostal, M. J., Li, X., Wang, T. D., Feehley, T., et al. (2017) · Science · doi:10.1126/science.aag2029 · Cited by 272 · see citing works
Sorbara, M. T., Dubin, K., Littmann, E. R., Moody, T. U., Fontana, E., Seok, R., Leiner, I. M., Taur, Y., Peled, J. U., van den Brink, M. R. M., et al. (2019) · Journal of Experimental Medicine · doi:10.1084/jem.20181639 · Cited by 259 · see citing works
Pan, F., Zhang, L., Li, M., Hu, Y., Zeng, B., Yuan, H., Zhao, L., & Zhang, C. (2018) · Microbiome · doi:10.1186/s40168-018-0440-5 · Cited by 237 · see citing works
McOrist, A. L., Miller, R. B., Bird, A. R., Keogh, J. B., Noakes, M., Topping, D. L., & Conlon, M. A. (2011) · The Journal of Nutrition · doi:10.3945/jn.110.128504 · Cited by 231 · see citing works
Datta, R., Platt, R., Yokoe, D. S., et al. (2011) · Archives of Internal Medicine · doi:10.1001/archinternmed.2011.64 · Cited by 213 · see citing works
Castillo, N. A., Perdigón, G., & de LeBlanc, A. D. M. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-177 · Cited by 211 · see citing works
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem
Solden, L., Naas, A. E., Roux, S., Daly, R. A., Collins, W., Nicora, C., Purvine, S. O., Hoyt, D. W., Schückel, J., Jørgensen, B., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0225-4 · Cited by 187 · see citing works
The Milieu Intérieur Consortium, Scepanovic, P., Hodel, F., Mondot, S., Partula, V., Byrd, A., Hammer, C., Alanio, C., Bergstedt, J., Patin, E., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0747-x · Cited by 171 · see citing works
Dietary l-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut
Kitamoto, S., Alteri, C. J., Rodrigues, M., Nagao‐Kitamoto, H., Sugihara, K., Himpsl, S. D., Bazzi, M., Miyoshi, M., Nishioka, T., Hayashi, A., et al. (2019) · Nature Microbiology · doi:10.1038/s41564-019-0591-6 · Cited by 154 · see citing works
Antibiotic Regimens and Intestinal Colonization with Antibiotic-Resistant Gram-Negative Bacilli
Donskey, C. J. (2006) · Clinical Infectious Diseases · doi:10.1086/504481 · Cited by 152 · see citing works
Shimasaki, T., Seekatz, A. M., Bassis, C. M., Rhee, Y., Yelin, R. D., Fogg, L., Dangana, T. E., Cisneros, E. C., Weinstein, R. A., Okamoto, K., et al. (2018) · Clinical Infectious Diseases · doi:10.1093/cid/ciy796 · Cited by 133 · see citing works
Sequeira, R. P., McDonald, J. A. K., Marchesi, J. R., & Clarke, T. B. (2020) · Nature Microbiology · doi:10.1038/s41564-019-0640-1 · Cited by 132 · see citing works
Oliveira, R. A., Ng, K. M., Correia, M. B., Cabral, V., Shi, H., Sonnenburg, J. L., Huang, K. C., & Xavier, K. B. (2020) · Nature Microbiology · doi:10.1038/s41564-019-0658-4 · Cited by 125 · see citing works
Self-citationKumar, M., Dhaka, P., Vijay, D., et al. (2016) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2016.05.014 · Cited by 102 · see citing works
Osbelt, L., Thiemann, S., Smit, N., Lesker, T. R., Schröter, M., Gálvez, E. J. C., Schmidt‐Hohagen, K., Pils, M. C., Mühlen, S., Dersch, P., et al. (2020) · PLoS Pathogens · doi:10.1371/journal.ppat.1008448 · Cited by 100 · see citing works
Probiotics as Drugs Against Human Gastrointestinal Infections
Sanz, Y., Nadal, I., & Sánchez, E. (2007) · Recent Patents on Anti-Infective Drug Discovery · doi:10.2174/157489107780832596 · Cited by 96 · see citing works
Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility
Barroso-Batista, J., Pedro, M. F., Sales-Dias, J., Pinto, C., Thompson, J. A., Pereira, H., Demengeot, J., Gordo, I., & Xavier, K. B. (2020) · Current Biology · doi:10.1016/j.cub.2020.01.050 · Cited by 86 · see citing works
Self-citationUrQt: an efficient software for the Unsupervised Quality trimming of NGS data
Modolo, L., & Lerat, E. (2015) · BMC Bioinformatics · doi:10.1186/s12859-015-0546-8 · Cited by 71 · see citing works
Park, J., Kato, K., Murakami, H., Hosomi, K., Tanisawa, K., Nakagata, T., Ohno, H., Konishi, K., Kawashima, H., Chen, Y.-A., et al. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02215-0 · Cited by 67 · see citing works
Itoh, K., & Freter, R. (1989) · Infection and Immunity · doi:10.1128/iai.57.2.559-565.1989 · Cited by 65 · see citing works
Rechenberger, J., Samaras, P., Jarząb, A., Behr, J., Frejno, M., Djuković, A., Sanz, J., González, E. M., Salavert, M., López-Hontangas, J. L., et al. (2019) · Proteomes · doi:10.3390/proteomes7010002 · Cited by 59 · see citing works
Self-citationGlowacki, R. W. P., Pudlo, N. A., Tunçil, Y. E., Luis, A. S., Sajjakulnukit, P., Terekhov, A. I., Lyssiotis, C. A., Hamaker, B. R., & Martens, E. C. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.11.009 · Cited by 59 · see citing works
Ljungquist, O., Kampmann, C., Resman, F., Riesbeck, K., & Tham, J. (2019) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2019.08.019 · Cited by 57 · see citing works
Jung, H.-J., Littmann, E. R., Seok, R., Leiner, I. M., Taur, Y., Peled, J. U., van den Brink, M. R. M., Ling, L., Chen, L., Kreiswirth, B. N., et al. (2019) · mBio · doi:10.1128/mbio.02663-18 · Cited by 52 · see citing works
Infections Due to Carbapenem-Resistant Bacteria in Patients With Hematologic Malignancies
Lalaoui, R., Javelle, É., Bakour, S., Úbeda, C., & Rolain, J. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01422 · Cited by 45 · see citing works
Self-citationThe Spanish gut microbiome reveals links between microorganisms and Mediterranean diet
Latorre‐Pérez, A., Hernández, M., Iglesias, J. R., Morán, J., Pascual, J., Porcar, M., Vilanova, C., & Yurrita, L. C. (2021) · Scientific Reports · doi:10.1038/s41598-021-01002-1 · Cited by 45 · see citing works
Piewngam, P., Quiñones, M., Thirakittiwatthana, W., Yungyuen, T., Otto, M. J., & Kiratisin, P. (2018) · International Journal of Antimicrobial Agents · doi:10.1016/j.ijantimicag.2018.12.006 · Cited by 44 · see citing works
Boix-Amorós, A., Hernández-Aguilar, M.-T., Artacho, A., Collado, M. C., & Mira, Á. (2020) · Scientific Reports · doi:10.1038/s41598-020-74719-0 · Cited by 44 · see citing works
Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae
Korach-Rechtman, H., Hreish, M., Fried, C., Gerassy-Vainberg, S., Azzam, Z. S., Kashi, Y., & Berger, G. (2020) · mSphere · doi:10.1128/msphere.00173-20 · Cited by 43 · see citing works
Measurement of Klebsiella Intestinal Colonization Density To Assess Infection Risk
Sun, Y., Patel, A., SantaLucia, J., Roberts, E., Zhao, L., Kaye, K. S., Rao, K. K., & Bachman, M. A. (2021) · mSphere · doi:10.1128/msphere.00500-21 · Cited by 39 · see citing works
Stecher, B. (2021) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2021.151484 · Cited by 37 · see citing works
Djuković, A., Garcia‐Garcerà, M., Martínez-Paredes, E. M., Isaac, S., Artacho, A., Martínez, J., & Úbeda, C. (2018) · Veterinary Research · doi:10.1186/s13567-018-0617-8 · Cited by 31 · see citing works
Woerther, P., Micol, J., Angebault, C., et al. (2015) · Journal of Medical Microbiology · doi:10.1099/jmm.0.000078 · Cited by 17 · see citing works
Copsel, S. N., Wolf, D., Komanduri, K. V., & Levy, R. B. (2019) · Haematologica · doi:10.3324/haematol.2018.198838 · Cited by 17 · see citing works
Almirón, M. A., Traglia, G. M., Rubio, A., & Sanjuan, N. A. (2013) · Current Microbiology · doi:10.1007/s00284-013-0367-9 · Cited by 16 · see citing works
Maziade, P.-J., Ship, N., Sniffen, J. C., & Goldstein, E. J. C. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab414 · Cited by 15 · see citing works
Kiyoshi, K., Kawashima, S., Nobuki, K., et al. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.02960-16 · Cited by 5 · see citing works
Djuković, A., González, E. M., Sanz, J., Artacho, A., Peñaranda, I., Herrera, B., Garzón, M. J., Salavert, M., López-Hontangas, J. L., Xavier, K. B., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01415-19 · Cited by 5 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Horrocks, V., King, O. G., Yip, A. Y. G., Marques, I. M., & McDonald, J. A. K. (2023) · Microbiology · doi:10.1099/mic.0.001377 · Cited by 104 · see citing works
Yip, A. Y. G., King, O. G., Omelchenko, O., Kurkimat, S., Horrocks, V., Mostyn, P., Danckert, N., Ghani, R., Satta, G., Jauneikaite, E., et al. (2023) · doi:10.1101/2023.03.25.533086 · Cited by 91 · see citing works
- Authors
- Djukovic, A., Garzón, M. J., Canlet, C., Cabral, V., Lalaoui, R., García-Garcerá, M., Rechenberger, J., Tremblay-Franco, M., Peñaranda, I., Puchades-Carrasco, L., Pineda-Lucena, A., González-Barberá, E. M., Salavert, M., López-Hontangas, J. L., Sanz, M. Á., Sanz, J., Kuster, B., Rolain, J.-M., Debrauwer, L., Xavier, K. B., Xavier, J. B., & Ubeda, C.
- Affiliations
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (ES)
- Université Toulouse III - Paul Sabatier (FR)
- Instituto Gulbenkian de Ciência (PT)
- Aix-Marseille Université (FR)
- Technical University of Munich (DE)
- Hospital Universitari i Politècnic La Fe (ES)
- Instituto de Investigación Sanitaria Aragón (ES)
- Instituto de Salud Carlos III (ES)
- ORCID
- Venue
- Nature Communications
- Published
- 2022-09-24
- Volume
- 13
- Issue
- 1
- Pages
- 5617-5617
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC9509339
- OpenAlex
- W4296977295
- Cited by
- 85
- References
- 76
- Citations by year
- 2026: 15 · 2025: 27 · 2024: 25 · 2023: 17 · 2022: 1
- FWCI
- 5.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- SERVAL (Université de Lausanne) (publishedVersion, cc-by)
- HAL (submittedVersion, cc-by)
- IRIS (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Hispana (submittedVersion, cc-by)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
- Funders
- European Commission (843183)
- Boehringer Ingelheim Fonds
- Agence Nationale de la Recherche (PCIN-2015-094, 11-INBS-010, ANR-10-LABX-0069, ANR-11-INBS-010, ANR-11-INBS, ANR-15-IFEC-0007, ANR-11-INBS-0010)
- Bundesministerium für Bildung und Forschung (031L0089, MSCA-IF-2018)
- Ministerio de Economía y Competitividad (PCIN-2015-094, PID2020)
- Ministerio de Ciencia e Innovación (PID2020, PID2020-120292RB-I00)
- National Institutes of Health
- Fundação para a Ciência e a Tecnologia
- Conselleria de Innovación, Universidades, Ciencia y Sociedad Digital, Generalitat Valenciana
- National Cancer Institute (P30CA008748)
- National Institute of Allergy and Infectious Diseases (R01AI137269)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- Lactobacillus, Clostridiales, multidrug-resistant Enterobacteriaceae, colonization resistance, gut microbiota, butyrate, Lactobacillus rhamnosus, Lactobacillus murinus, probiotics, antibiotic-induced dysbiosis, hospitalized patients
- MeSH terms
- Clostridiales, Eubacteriales, Animals, Anti-Bacterial Agents, Butyrates, Enterobacteriaceae, Lactobacillus, Prospective Studies, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
