{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T06:11:41Z","timestamp":1791094301333,"version":"4.1.0"},"reference-count":63,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2014,3,18]],"date-time":"2014-03-18T00:00:00Z","timestamp":1395100800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"},{"start":{"date-parts":[[2014,5,1]],"date-time":"2014-05-01T00:00:00Z","timestamp":1398902400000},"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":["mBio"],"published-print":{"date-parts":[[2014,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The\n            <jats:italic>Salmonella<\/jats:italic>\n            genus comprises a group of pathogens associated with illnesses ranging from gastroenteritis to typhoid fever. We performed an\n            <jats:italic>in silico<\/jats:italic>\n            analysis of comparatively reannotated\n            <jats:italic>Salmonella<\/jats:italic>\n            genomes to identify genomic signatures indicative of disease potential. By removing numerous annotation inconsistencies and inaccuracies, the process of reannotation identified a network of 469 genes involved in central anaerobic metabolism, which was intact in genomes of gastrointestinal pathogens but degrading in genomes of extraintestinal pathogens. This large network contained pathways that enable gastrointestinal pathogens to utilize inflammation-derived nutrients as well as many of the biochemical reactions used for the enrichment and biochemical discrimination of\n            <jats:italic>Salmonella<\/jats:italic>\n            serovars. Thus, comparative genome analysis identifies a metabolic network that provides clues about the strategies for nutrient acquisition and utilization that are characteristic of gastrointestinal pathogens.\n          <\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            While some\n            <jats:italic>Salmonella<\/jats:italic>\n            serovars cause infections that remain localized to the gut, others disseminate throughout the body. Here, we compared\n            <jats:italic>Salmonella<\/jats:italic>\n            genomes to identify characteristics that distinguish gastrointestinal from extraintestinal pathogens. We identified a large metabolic network that is functional in gastrointestinal pathogens but decaying in extraintestinal pathogens. While taxonomists have used traits from this network empirically for many decades for the enrichment and biochemical discrimination of\n            <jats:italic>Salmonella<\/jats:italic>\n            serovars, our findings suggest that it is part of a \u201cbusiness plan\u201d for growth in the inflamed gastrointestinal tract. By identifying a large metabolic network characteristic of\n            <jats:italic>Salmonella<\/jats:italic>\n            serovars associated with gastroenteritis, our\n            <jats:italic>in silico<\/jats:italic>\n            analysis provides a blueprint for potential strategies to utilize inflammation-derived nutrients and edge out competing gut microbes.\n          <\/jats:p>","DOI":"10.1128\/mbio.00929-14","type":"journal-article","created":{"date-parts":[[2014,3,19]],"date-time":"2014-03-19T01:33:29Z","timestamp":1395192809000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":162,"title":["Comparative Analysis of\n            <i>Salmonella<\/i>\n            Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut"],"prefix":"10.1128","volume":"5","author":[{"given":"Sean-Paul","family":"Nuccio","sequence":"first","affiliation":[{"name":"Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas J.","family":"B\u00e4umler","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/35097083"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/35101607"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2001-2-8-reviews1023"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf566"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0931379100"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng1470"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02156850"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.47848-0"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.73.6.3358-3366.2005"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-5822.2008.01118.x"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1003267"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.58.1.137-143.1990"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.60.2.491-496.1992"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00297-11"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.67.9.4879-4885.1999"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature09415"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00143-12"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2011.10.002"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.72.11.6294-6299.2004"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2013.11.002"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1107857108"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.183.8.2463-2475.2001"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0067155"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1038\/502S96a"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.12318"},{"key":"e_1_3_2_27_2","first-page":"434","article-title":"Un nouveau milieu d\u2019enrichissement pour la recherche du Bacille Typhique at Paratyphique","volume":"89","author":"Muller L","year":"1923","unstructured":"MullerL . 1923. 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