Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites
Open accessAbstract
The intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. We used ex vivo faecal cultures to measure the impact of antibiotics (that promote CRE intestinal colonisation) on the faecal microbiota from healthy human donors. We demonstrated that antibiotics decreased the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales ) in human faecal microbiota, resulting in an enrichment of nutrients and a depletion of microbial metabolites. We measured the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several carbapenem-resistant Enterobacteriaceae strains, including Escherichia coli , Klebsiella pneumoniae , and Enterobacter hormaechei . Nutrients (which were elevated with antibiotics) acted as carbon and nitrogen sources to support CRE growth, where CRE strains showed an ordered preference for specific nutrients. These nutrients were also increased in faeces from antibiotic-treated mice but decreased following intestinal colonisation with carbapenem-resistant E. coli . Microbial metabolites (which decreased with antibiotics) were inhibitory towards CRE growth in vitro . Carbapenem-resistant E. coli growth was decreased in faecal samples from mice treated with a mixture of inhibitory metabolites compared with PBS-treated mice. These findings demonstrated that killing gut commensals with antibiotics disrupts colonisation resistance by enriching nutrients that support CRE growth and depleting metabolites that inhibit CRE growth. These results support the development of new microbiome therapeutics to prevent CRE intestinal colonisation, which would also prevent the subsequent development of invasive CRE infections.
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?
Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments.
“Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments and also have a different order of nutrient preference [79, 128].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [79]
Different species of Enterobacteriaceae have a different order of nutrient preference.
“Different species of Enterobacteriaceae have different nutrient utilization profiles in aerobic and anaerobic environments and also have a different order of nutrient preference [79, 128].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [79]
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
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
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
QUAST: quality assessment tool for genome assemblies
Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt086 · Cited by 11,172 · 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
Wiegand, I., Hilpert, K., & Hancock, R. E. W. (2008) · Nature Protocols · doi:10.1038/nprot.2007.521 · Cited by 6,156 · see citing works
Identification of acquired antimicrobial resistance genes
Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F. M., & Larsen, M. V. (2012) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dks261 · Cited by 4,980 · see citing works
The antibiotic resistance crisis: part 1: causes and threats.
Ventola, C. L. (2015) · PubMed Central · Cited by 4,558 · see citing works
ResFinder 4.0 for predictions of phenotypes from genotypes
Bortolaia, V., Kaas, R. S., Ruppe, E., Roberts, M. C., Schwarz, S., Cattoir, V., Philippon, A., Allesoe, R. L., Rebelo, A. R., Florensa, A. F., et al. (2020) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkaa345 · Cited by 3,373 · see citing works
Short chain fatty acids in human large intestine, portal, hepatic and venous blood
Cummings, J. H., Pomare, E. W., Branch, W. J., Naylor, C. P., & Macfarlane, G. T. (1987) · Gut · doi:10.1136/gut.28.10.1221 · Cited by 3,119 · see citing works
BIGSdb: Scalable analysis of bacterial genome variation at the population level
Jolley, K. A., & Maiden, M. C. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-595 · Cited by 2,341 · see citing works
<p>Antimicrobial Resistance: Implications and Costs</p>
Dadgostar, P. (2019) · Infection and Drug Resistance · doi:10.2147/idr.s234610 · Cited by 2,024 · see citing works
Kelly, C. J., Zheng, L., Campbell, E. L., Saeedi, B., Scholz, C. C., Bayless, A. J., Wilson, K. E., Glover, L. E., Kominsky, D. J., Magnuson, A., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.03.005 · Cited by 1,716 · see citing works
Oliphant, K., & Allen-Vercoe, E. (2019) · Microbiome · doi:10.1186/s40168-019-0704-8 · Cited by 1,327 · see citing works
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035 · 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
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
Carbohydrate metabolism in Bifidobacteria
Pokusaeva, K., Fitzgerald, G. F., & van Sinderen, D. (2011) · Genes & Nutrition · doi:10.1007/s12263-010-0206-6 · Cited by 855 · see citing works
Regulation of Intestinal Barrier Function by Microbial Metabolites
Ghosh, S., Whitley, C. S., Haribabu, B., & Jala, V. R. (2021) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2021.02.007 · Cited by 835 · see citing works
The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens
Kim, S., Covington, A., & Pamer, E. G. (2017) · Immunological Reviews · doi:10.1111/imr.12563 · Cited by 741 · see citing works
Inulin and Oligofructose: What Are They?
Niness, K. (1999) · Journal of Nutrition · doi:10.1093/jn/129.7.1402s · Cited by 713 · see citing works
Carbon nutrition of Escherichia coli in the mouse intestine
Chang, D., Smalley, D. J., Tucker, D. L., Leatham, M. P., Norris, W. E., Stevenson, S. J., Anderson, A. B., Grissom, J. E., Laux, D. C., Cohen, P. S., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307888101 · Cited by 513 · 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
Ferreyra, J. A., Wu, K. J., Hryckowian, A. J., Bouley, D. M., Weimer, B. C., & Sonnenburg, J. L. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.003 · Cited by 382 · see citing works
Ianiro, G., Punčochář, M., Karcher, N., Porcari, S., Armanini, F., Asnicar, F., Beghini, F., Blanco-Míguez, A., Cumbo, F., Manghi, P., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01964-3 · Cited by 366 · see citing works
Fachi, J. L., Felipe, J. D. S., Pral, L. P., da Silva, B. K., Corrêa, R. O., de Andrade, M. C. P., da Fonseca, D. M., Basso, P. J., Câmara, N. O. S., de Sales e Souza, É. L., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.054 · Cited by 364 · see citing works
Resistant starch: impact on the gut microbiome and health
DeMartino, P., & Cockburn, D. W. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.10.008 · Cited by 363 · see citing works
Advances and perspectives in in vitro human gut fermentation modeling
Payne, A. N., Zihler, A., Chassard, C., & Lacroix, C. (2011) · Trends in biotechnology · doi:10.1016/j.tibtech.2011.06.011 · Cited by 340 · see citing works
Visualising associations between paired ‘omics’ data sets
González, I., Cao, K. L., Davis, M. J., & Dejean, S. (2012) · BioData Mining · doi:10.1186/1756-0381-5-19 · Cited by 316 · see citing works
Oxygen as a driver of gut dysbiosis
Rivera-Chávez, F., Lopez, C. A., & Bäumler, A. J. (2016) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.09.022 · Cited by 311 · see citing works
Smith, E. A., & Macfarlane, G. T. (1998) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.1998.tb00487.x · Cited by 277 · 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
Xylan structure, microbial xylanases, and their mode of action
Bastawde, K. B. (1992) · World Journal of Microbiology and Biotechnology · doi:10.1007/bf01198746 · Cited by 257 · see citing works
Krych, Ł., Hansen, C. H. F., Hansen, A. K., van den Berg, F. W. J., & Nielsen, D. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062578 · Cited by 250 · see citing works
Contribution of the microflora to proteolysis in the human large intestine
Macfarlane, G. T., Allison, C., Gibson, S. A. W., & Cummings, J. H. (1988) · Journal of Applied Bacteriology · doi:10.1111/j.1365-2672.1988.tb02427.x · Cited by 237 · see citing works
Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health
Ríos-Covián, D., Salazar, N., Gueimonde, M., & Reyes‐Gavilán, C. G. D. L. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00376 · Cited by 230 · see citing works
Kaya, M., Sousa, A. G., Crépeau, M., Sørensen, S. O., & Ralet, M. (2014) · Annals of Botany · doi:10.1093/aob/mcu150 · Cited by 213 · see citing works
Intestinal microbiota in metabolic diseases
Clavel, T., Desmarchelier, C., Haller, D., Gérard, P., Rohn, S., Lepage, P., & Daniel, H. (2014) · Gut Microbes · doi:10.4161/gmic.29331 · Cited by 195 · see citing works
McDonald, J. A. K., Mullish, B. H., Pechlivanis, A., Liu, Z., Brignardello, J., Kao, D. H., Holmes, E. C., Li, J. V., Clarke, T. B., Thursz, M. R., et al. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.07.014 · Cited by 189 · see citing works
Self-citationStarch Digestion by Gut Bacteria: Crowdsourcing for Carbs
Cerqueira, F. M., Photenhauer, A. L., Pollet, R. M., Brown, H. A., & Koropatkin, N. M. (2019) · Trends in Microbiology · doi:10.1016/j.tim.2019.09.004 · Cited by 186 · see citing works
McDonald, J. A. K., Schroeter, K., Fuentes, S., Jong, I. H., Khursigara, C. M., de Vos, W. M., & Allen‐Vercoe, E. (2013) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2013.08.008 · Cited by 178 · see citing works
Self-citationMortensen, P. B., Holtug, K., & Rasmussen, H. S. (1988) · Journal of Nutrition · doi:10.1093/jn/118.3.321 · Cited by 169 · see citing works
Tunçil, Y. E., Xiao, Y., Porter, N. T., Reuhs, B. L., Martens, E. C., & Hamaker, B. R. (2017) · mBio · doi:10.1128/mbio.01068-17 · Cited by 162 · see citing works
Stewardson, A. J., Gaïa, N., François, P., Malhotra-Kumar, S., Delémont, C., de Tejada, B. M., Schrenzel, J., Harbarth, S., & Lazarević, V. (2014) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2014.11.016 · Cited by 142 · see citing works
der Meulen, R. V., Adriany, T., Verbrugghe, K., & Vuyst, L. D. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.00146-06 · Cited by 141 · see citing works
Kageyama, A., Benno, Y., & Nakase, T. (1999) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-49-2-557 · Cited by 131 · see citing works
(1999) · PubMed · Cited by 120 · see citing works
Casein utilization by lactococci
Smid, E. J., Poolman, B., & Konings, W. N. (1991) · Applied and Environmental Microbiology · doi:10.1128/aem.57.9.2447-2452.1991 · Cited by 119 · see citing works
Manges, A. R., Steiner, T. S., & Wright, A. J. (2016) · Scandinavian Journal of Infectious Diseases · doi:10.1080/23744235.2016.1177199 · Cited by 117 · see citing works
Trehalose accumulation from soluble starch by Saccharomycopsis fibuligera sdu
Chi, Z., Liu, J., & Zhang, W. (2001) · Enzyme and Microbial Technology · doi:10.1016/s0141-0229(00)00318-5 · Cited by 116 · see citing works
Pletz, M. W., Rau, M., Bulitta, J. B., Roux, A. D., Burkhardt, O., Kruse, G., Kurowski, M., Nord, C. E., & Lode, H. M. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.10.3765-3772.2004 · Cited by 112 · see citing works
Mullish, B. H., Pechlivanis, A., Barker, G. F., Thursz, M. R., Marchesi, J. R., & McDonald, J. A. K. (2018) · Methods · doi:10.1016/j.ymeth.2018.04.028 · Cited by 106 · see citing works
Self-citationMetagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota
Vital, M., Howe, A., Bergeron, N., Krauss, R. M., Jansson, J. K., & Tiedje, J. M. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.01562-18 · Cited by 98 · see citing works
Phenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria
Pudlo, N. A., Urs, K., Crawford, R., Pirani, A. M., Atherly, T. A., Jimenez, R., Terrapon, N., Henrissat, B., Peterson, D. A., Ziemer, C. J., et al. (2022) · mSystems · doi:10.1128/msystems.00947-21 · Cited by 94 · see citing works
Reingestion of feces in rodents and its daily rhythmicity
Kenagy, G. J., & Hoyt, D. F. (1979) · Oecologia · doi:10.1007/bf00545245 · Cited by 90 · see citing works
Park, S.-Y., Rao, C., Coyte, K. Z., Kuziel, G. A., Zhang, Y., Huang, W., Franzosa, E. A., Weng, J., Huttenhower, C., & Rakoff-Nahoum, S. (2022) · Cell · doi:10.1016/j.cell.2022.01.002 · Cited by 85 · see citing works
Djukovic, A., Garzón, M. J., Canlet, C., Cabral, V., Lalaoui, R., García-Garcerá, M., Rechenberger, J., Tremblay-Franco, M., Peñaranda, I., Puchades-Carrasco, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33313-w · Cited by 85 · see citing works
Pérez, F., Pultz, M. J., Endimiani, A., Bonomo, R. A., & Donskey, C. J. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00891-10 · Cited by 81 · see citing works
High-throughput analysis of the impact of antibiotics on the human intestinal microbiota composition
Ladirat, S. E., Schols, H. A., Nauta, A., Schoterman, M. H. C., Keijser, B. J. F., Montijn, R. C., Gruppen, H., & Schuren, F. H. J. (2012) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2012.12.011 · Cited by 80 · see citing works
Characterization of the Serpin-Encoding Gene ofBifidobacterium breve210B
Turroni, F., Foroni, E., Motherway, M. O., Bottacini, F., Giubellini, V., Zomer, A., Ferrarini, A., Delledonne, M., Zhang, Z., van Sinderen, D., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02938-09 · Cited by 75 · see citing works
Pharmacokinetics of Meropenem in Animals, Healthy Volunteers, and Patients
Moon, Y. S. K., Chung, K. C., & Gill, M. A. (1997) · Clinical Infectious Diseases · doi:10.1093/clinids/24.supplement_2.s249 · Cited by 71 · see citing works
Kantele, A., Kuenzli, E., Dunn, S. J., Dance, D. A. B., Newton, P. N., Davong, V., Mero, S., Pakkanen, S. H., Neumayr, A. L. C., Hatz, C., et al. (2021) · The Lancet Microbe · doi:10.1016/s2666-5247(20)30224-x · Cited by 71 · see citing works
Burdet, C., Grall, N., Linard, M., Bridier‐Nahmias, A., Benhayoun, M., Bourabha, K., Magnan, M., Clermont, O., d’Humières, C., Tenaillon, O., et al. (2019) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02244-18 · Cited by 70 · see citing works
Increasing the Sensitivity of Magnetic Resonance Spectroscopy and Imaging
WEBB, A. G. (2011) · Analytical Chemistry · doi:10.1021/ac201500v · Cited by 68 · see citing works
AMiGA: Software for Automated Analysis of Microbial Growth Assays
Midani, F. S., Collins, J., & Britton, R. A. (2021) · mSystems · doi:10.1128/msystems.00508-21 · Cited by 65 · see citing works
Shelton, C. D., Yoo, W., Shealy, N. G., Torres, T. P., Zieba, J. K., Calcutt, M. W., Foegeding, N. J., Kim, D., Kim, J., Ryu, S., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2021.110180 · Cited by 65 · see citing works
Autieri, S. M., Lins, J. J., Leatham, M. P., Laux, D. C., Conway, T., & Cohen, P. S. (2007) · Infection and Immunity · doi:10.1128/iai.00822-07 · Cited by 54 · see citing works
Effect of meropenem on the intestinal microflora
Bergan, T., Nord, C. E., & Thorsteinsson, S. B. (1991) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/bf01963943 · Cited by 52 · see citing works
Brismar, B., Edlund, C., Malmborg, A. S., et al. (1990) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.34.3.481 · Cited by 48 · see citing works
Fernandez-Julia, P., Commane, D. M., van Sinderen, D., & Muñoz-Muñoz, J. (2022) · Microbiome Research Reports · doi:10.20517/mrr.2021.05 · Cited by 45 · see citing works
Effects of valerate on intestinal barrier function in cultured Caco-2 epithelial cell monolayers
Gao, G., Zhou, J., Wang, H., Ding, Y., Zhou, J., Chong, P. H., Zhu, L., Ke, L., Wang, X., Rao, P., et al. (2022) · Molecular Biology Reports · doi:10.1007/s11033-021-06991-w · Cited by 40 · see citing works
Reed, A. D., & Theriot, C. M. (2021) · Microorganisms · doi:10.3390/microorganisms9020371 · Cited by 39 · see citing works
Effect of piperacillin/tazobactam treatment on human bowel microflora
Nord, C. E., Brismar, B., Kasholm-Tengve, B., & Tunevall, G. (1993) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/31.suppl_a.61 · Cited by 38 · see citing works
Imipenem concentrations in colorectal surgery and impact on the colonic microflora
Kager, L., Brismar, B., Malmborg, A. S., et al. (1989) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.33.2.204 · Cited by 36 · see citing works
Kang, J. T. L., Teo, J. J. Y., Bertrand, D., Ng, A. H. Q., Ravikrishnan, A., Yong, M., Ng, O. T., Marimuthu, K., Chen, S. L., Chng, K. R., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01221-w · Cited by 35 · see citing works
Experimental replications in animal trials
Frommlet, F., & Heinze, G. (2020) · Laboratory Animals · doi:10.1177/0023677220907617 · Cited by 32 · see citing works
The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal
Engevik, M. A., Danhof, H. A., Hall, A., Engevik, K. A., Horvath, T. D., Haidacher, S. J., Hoch, K. M., Endres, B. T., Bajaj, M., Garey, K. W., et al. (2021) · BMC Microbiology · doi:10.1186/s12866-021-02166-6 · Cited by 32 · see citing works
Pultz, N. J., Hoskins, L. C., & Donskey, C. J. (2006) · Microbial Drug Resistance · doi:10.1089/mdr.2006.12.63 · Cited by 31 · see citing works
Venturini, C., Bowring, B. G., Fajardo-Lubian, A., Devine, C., & Iredell, J. R. (2020) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01504-20 · Cited by 23 · see citing works
THE EFFECT OF TEMPERATURE ON THE RATE OF HYDROLYSIS OF TRIGLYCERIDES BY PANCREATIC LIPASE
Schwartz, B. (1943) · The Journal of General Physiology · doi:10.1085/jgp.27.2.113 · Cited by 15 · see citing works
Assaf, A., Grangé, E., Cordella, C., et al. (2020) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-020-02596-7 · Cited by 8 · see citing works
Modeling the bacterial dynamics in the gut microbiota following an antibiotic‐induced perturbation
Guk, J., Bridier‐Nahmias, A., Magnan, M., Grall, N., Duval, X., Clermont, O., Ruppé, É., d’Humières, C., Tenaillon, O., Denamur, É., et al. (2022) · CPT Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12806 · Cited by 7 · see citing works
Silva, C. H. P. D. M. E. (2000) · Brazilian Journal of Microbiology · doi:10.1590/s1517-83822000000400006 · Cited by 4 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- [53]Raja Makendran Nandan Raja Rajendran. Enzymatic conversion of RNA from yeast extract to guanosine monophosphate (a flavoring agent). Master’s thesis, Chalmers University of Technology https://odr.chalmers.se/handle/20.500.12380/166692 (2012).
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
Self-citation
- Authors
- Yip, A. Y. G., King, O. G., Omelchenko, O., Kurkimat, S., Horrocks, V., Mostyn, P., Danckert, N., Ghani, R., Satta, G., Jauneikaite, E., Davies, F. J., Clarke, T. B., Mullish, B. H., Marchesi, J. R., & McDonald, J. A. K.
- Affiliations
- Imperial College London (GB)
- St Mary's Hospital (GB)
- Imperial College Healthcare NHS Trust (GB)
- University College London (GB)
- National Institute for Health and Care Research (GB)
- Corresponding author
- McDonald, Julie A. K.
- ORCID
- Venue
- Nature Communications
- Publisher
- openRxiv
- Published
- 2023-03-25
- Volume
- 14
- Issue
- 1
- Pages
- 5094-5094
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10444851
- OpenAlex
- W4386070166
- Cited by
- 91
- References
- 82
- Citations by year
- 2026: 24 · 2025: 32 · 2024: 33 · 2023: 2
- FWCI
- 8.11
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Spiral (Imperial College London) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (107660/Z/15/Z)
- UK Research and Innovation (MR/X502959/1)
- National Institute for Health Research Health Protection Research Unit
- National Institute for Health and Care Research (CL‐2019‐21‐002)
- University of Warwick
- Imperial College London
- Imperial College Healthcare NHS Trust
- University of Oxford
- Rosetrees Trust
- Medical Research Council (MR/W025655/1, 2288243, MR/X502959/1, MR/T005254/1, MR/X020258/1)
- NIHR Imperial Biomedical Research Centre
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Antibiotic Use and Resistance
- Keywords
- carbapenem-resistant Enterobacteriaceae, carbapenem-resistant Escherichia coli, broad-spectrum antibiotics, gut microbiota, antibiotic-induced dysbiosis, intestinal colonization, nutrient enrichment, microbial metabolites, inhibitory metabolites, Bifidobacteriaceae, Bacteroidales, gut commensals
- MeSH terms
- Carbapenem-Resistant Enterobacteriaceae, Nutrients, Animals, Anti-Bacterial Agents, Escherichia coli, Humans, Intestinal Neoplasms, Actinobacteria, Bacteroidetes, 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
