{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T20:12:23Z","timestamp":1767730343338,"version":"build-2238731810"},"reference-count":76,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2013,10,1]],"date-time":"2013-10-01T00:00:00Z","timestamp":1380585600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Infect Immun"],"published-print":{"date-parts":[[2013,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Clostridium difficile<\/jats:named-content>\n                    is currently the major cause of nosocomial intestinal diseases associated with antibiotic therapy in adults. In order to improve our knowledge of\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    -host interactions, we analyzed the genome-wide temporal expression of\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    630 genes during the first 38 h of mouse colonization to identify genes whose expression is modulated\n                    <jats:italic>in vivo<\/jats:italic>\n                    , suggesting that they may play a role in facilitating the colonization process. In the ceca of the\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    -monoassociated mice, 549 genes of the\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    genome were differentially expressed compared to their expression during\n                    <jats:italic>in vitro<\/jats:italic>\n                    growth, and they were distributed in several functional categories. Overall, our results emphasize the roles of genes involved in host adaptation. Colonization results in a metabolic shift, with genes responsible for the fermentation as well as several other metabolic pathways being regulated inversely to those involved in carbon metabolism. In addition, several genes involved in stress responses, such as ferrous iron uptake or the response to oxidative stress, were regulated\n                    <jats:italic>in vivo<\/jats:italic>\n                    . Interestingly, many genes encoding conserved hypothetical proteins (CHP) were highly and specifically upregulated\n                    <jats:italic>in vivo<\/jats:italic>\n                    . Moreover, genes for all stages of sporulation were quickly induced\n                    <jats:italic>in vivo<\/jats:italic>\n                    , highlighting the observation that sporulation is central to the persistence of\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    in the gut and to its ability to spread in the environment. Finally, we inactivated two genes that were differentially expressed\n                    <jats:italic>in vivo<\/jats:italic>\n                    and evaluated the relative colonization fitness of the wild-type and mutant strains in coinfection experiments. We identified a CHP as a putative colonization factor, supporting the suggestion that the\n                    <jats:italic>in vivo<\/jats:italic>\n                    transcriptomic approach can unravel new\n                    <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. difficile<\/jats:named-content>\n                    virulence genes.\n                  <\/jats:p>","DOI":"10.1128\/iai.00515-13","type":"journal-article","created":{"date-parts":[[2013,7,29]],"date-time":"2013-07-29T23:01:12Z","timestamp":1375138872000},"page":"3757-3769","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":137,"title":["Adaptive Strategies and Pathogenesis of Clostridium difficile from\n                    <i>In Vivo<\/i>\n                    Transcriptomics"],"prefix":"10.1128","volume":"81","author":[{"given":"Claire","family":"Janoir","sequence":"first","affiliation":[{"name":"EA 4043, Universit\u00e9 Paris-Sud 11, Facult\u00e9 de Pharmacie, Ch\u00e2tenay-Malabry, France"}]},{"given":"C\u00e9cile","family":"Den\u00e8ve","sequence":"additional","affiliation":[{"name":"EA 4043, Universit\u00e9 Paris-Sud 11, Facult\u00e9 de Pharmacie, Ch\u00e2tenay-Malabry, France"}]},{"given":"Sylvie","family":"Bouttier","sequence":"additional","affiliation":[{"name":"EA 4043, Universit\u00e9 Paris-Sud 11, Facult\u00e9 de Pharmacie, Ch\u00e2tenay-Malabry, France"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Barbut","sequence":"additional","affiliation":[{"name":"Centre National de R\u00e9f\u00e9rence de Clostridium difficile, Service de Microbiologie, H\u00f4pital Saint-Antoine, Assistance Publique-H\u00f4pitaux de Paris, Paris, France"}]},{"given":"Sandra","family":"Hoys","sequence":"additional","affiliation":[{"name":"EA 4043, Universit\u00e9 Paris-Sud 11, Facult\u00e9 de Pharmacie, Ch\u00e2tenay-Malabry, France"}]},{"given":"Laxmee","family":"Caleechum","sequence":"additional","affiliation":[{"name":"Laboratoire Pathogen\u00e8se des Bact\u00e9ries Ana\u00e9robies, D\u00e9partement de Microbiologie, Institut Pasteur, Paris, France"}]},{"given":"Diana","family":"Chapet\u00f3n-Montes","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Recherche et d'Expertise Bact\u00e9ries Ana\u00e9robies et Toxines, D\u00e9partement de Microbiologie, Institut Pasteur, Paris, France"}]},{"given":"F\u00e1tima C.","family":"Pereira","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Oeiras, Portugal"}]},{"given":"Adriano O.","family":"Henriques","sequence":"additional","affiliation":[{"name":"Instituto de Tecnologia Qu\u00edmica e Biol\u00f3gica, Universidade Nova de Lisboa, Oeiras, Portugal"}]},{"given":"Anne","family":"Collignon","sequence":"additional","affiliation":[{"name":"EA 4043, Universit\u00e9 Paris-Sud 11, Facult\u00e9 de Pharmacie, Ch\u00e2tenay-Malabry, France"},{"name":"Service de Microbiologie, H\u00f4pital Jean Verdier, Assistance Publique-H\u00f4pitaux de Paris, Paris, France"}]},{"given":"Marc","family":"Monot","sequence":"additional","affiliation":[{"name":"Laboratoire Pathogen\u00e8se des Bact\u00e9ries Ana\u00e9robies, D\u00e9partement de Microbiologie, Institut Pasteur, Paris, France"}]},{"given":"Bruno","family":"Dupuy","sequence":"additional","affiliation":[{"name":"Laboratoire Pathogen\u00e8se des Bact\u00e9ries Ana\u00e9robies, D\u00e9partement de Microbiologie, Institut Pasteur, Paris, France"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2164"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00445-10"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-9-r102"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0924-8579(09)70012-3"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2008.00103.x"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.73.3.1797-1810.2005"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.47657-0"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1086\/653484"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jir112"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2007.05.021"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2006.05315.x"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00272-11"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.febslet.2004.07.055"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1046-2023(03)00155-5"},{"key":"e_1_3_3_16_2","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini C","year":"1995","unstructured":"BenjaminiCHochbergYY. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57:289\u2013300.","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.28.1.277-282.1980"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.173.6.4137"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1099\/00222615-40-2-102"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng1830"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000449"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-7-2245"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.1998.00663.x"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.70.10.5770-5778.2002"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.028472-0"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1462-5822.2001.00152.x"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.2353\/ajpath.2006.060112"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00578-07"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002024"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.43.10.5018-5025.2005"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00558-09"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.69.12.7937-7940.2001"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.05305-11"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibs.2006.01.007"},{"key":"e_1_3_3_35_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M111.259150"},{"key":"e_1_3_3_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00651-10"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.70.12.7176-7178.2002"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2008.06463.x"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00019-11"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01098-08"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature09488"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01208-08"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00030-10"},{"key":"e_1_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.051565-0"},{"key":"e_1_3_3_45_2","first-page":"G822","article-title":"Luminal glucose concentrations in the gut under normal conditions","volume":"259","author":"Ferraris RP","year":"1990","unstructured":"FerrarisRPYasharpourSLloydKCMirzayanRDiamondJM. 1990. Luminal glucose concentrations in the gut under normal conditions. Am. J. Physiol. 259:G822\u2013G837.","journal-title":"Am. J. Physiol."},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.10.5881-5888.2000"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.7.2099-2106.2004"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks864"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01370-06"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.56.10.2610-2614.1988"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2012.02841.x"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.68.2.234-262.2004"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00882-09"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.micro.61.080706.093224"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.02181-12"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01482-07"},{"key":"e_1_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000566"},{"key":"e_1_3_3_58_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00147-12"},{"key":"e_1_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1006\/anae.1995.1025"},{"key":"e_1_3_3_60_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.anaerobe.2012.04.007"},{"key":"e_1_3_3_61_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10534-006-0003-2"},{"key":"e_1_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00052-06"},{"key":"e_1_3_3_63_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2012.06.027"},{"key":"e_1_3_3_64_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.abb.2012.04.014"},{"key":"e_1_3_3_65_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.022756-0"},{"key":"e_1_3_3_66_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0020076"},{"key":"e_1_3_3_67_2","doi-asserted-by":"publisher","DOI":"10.1021\/pr200327t"},{"key":"e_1_3_3_68_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.8511586"},{"key":"e_1_3_3_69_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6976.2008.00148.x"},{"key":"e_1_3_3_70_2","doi-asserted-by":"publisher","DOI":"10.1111\/cmi.12139"},{"key":"e_1_3_3_71_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0056051"},{"key":"e_1_3_3_72_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00217-12"},{"key":"e_1_3_3_73_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1002954"},{"key":"e_1_3_3_74_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00260-11"},{"key":"e_1_3_3_75_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02275-12"},{"key":"e_1_3_3_76_2","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.12.64"},{"key":"e_1_3_3_77_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01209-09"}],"updated-by":[{"DOI":"10.1128\/iai.01408-13","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2014,1,22]],"date-time":"2014-01-22T00:00:00Z","timestamp":1390348800000}}],"container-title":["Infection and Immunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00515-13","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00515-13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,15]],"date-time":"2024-05-15T12:30:58Z","timestamp":1715776258000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/IAI.00515-13"}},"subtitle":[],"editor":[{"given":"A. J.","family":"B\u00e4umler","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,10]]},"references-count":76,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2013,10]]}},"alternative-id":["10.1128\/IAI.00515-13"],"URL":"https:\/\/doi.org\/10.1128\/iai.00515-13","relation":{},"ISSN":["0019-9567","1098-5522"],"issn-type":[{"value":"0019-9567","type":"print"},{"value":"1098-5522","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,10]]},"assertion":[{"value":"2013-04-25","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-07-19","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2013-09-16","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}