Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments
Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locat...
Gespeichert in:
| Veröffentlicht in: | PloS one 2016-02, Vol.11 (2), p.e0149423-e0149423 |
|---|---|
| Hauptverfasser: | , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e0149423 |
|---|---|
| container_issue | 2 |
| container_start_page | e0149423 |
| container_title | PloS one |
| container_volume | 11 |
| creator | Ding, Tong Case, Kyle A Omolo, Morrine A Reiland, Holly A Metz, Zachary P Diao, Xinyu Baumler, David J |
| description | Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes. |
| doi_str_mv | 10.1371/journal.pone.0149423 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1765911025</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A443510473</galeid><doaj_id>oai_doaj_org_article_87508b7c086248a797155cdcc0f00674</doaj_id><sourcerecordid>A443510473</sourcerecordid><originalsourceid>FETCH-LOGICAL-c585t-7c50c2ef19e5600388250d49597c341629a9666edc497548a940cf3a2dffea123</originalsourceid><addsrcrecordid>eNptkt1qFDEUgAdRbK2-geiAIN7smv9MboSyrN1C1UL1OmQzmd2UTLJNMgVfwOc2052WXfEqYc53vnNO5lTVWwjmEHP4-TYM0Ss33wVv5gASQRB-Vp1CgdGMIYCfH9xPqlcp3QJAccPYy-oEsaahjJLT6s91NK3V2fpNvUzJ-GyVq7-ZrNbBWV1fGB96Uy-CzyVWh67-bvXWzG52RtuuAMsSiGGtdDnG1NXQK19fq7wNG-NT3Q5xdN_YfnAq2-BHxyqkXDLvbQy-L970unrRKZfMm-k8q359Xf5crGZXPy4uF-dXM00bmmdcU6CR6aAwlAGAmwZR0BJBBdeYQIaEEowx02oiOCWNEgToDivUdp1REOGz6v3eu3MhyekJk4ScUQEhQLQQl3uiDepW7qLtVfwtg7Ly4UOIG6littoZ2XAKmjXXoGGo1OKCQ0p1qzXoAGCcFNeXqdqw7ktTZdKo3JH0OOLtVm7CvSSclvZxEXyaBDHcDSZl2dukjXPKmzA89M0Bx5TBgn74B_3_dBO1UWUA67tQ6upRKs8JwRQCwseyHw-orVEub1Nww_j70jFI9qCOIaVouqfZIJDjlj42IcctldOWlrR3h-_ylPS4lvgvCh_koQ</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1765911025</pqid></control><display><type>article</type><title>Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Ding, Tong ; Case, Kyle A ; Omolo, Morrine A ; Reiland, Holly A ; Metz, Zachary P ; Diao, Xinyu ; Baumler, David J</creator><creatorcontrib>Ding, Tong ; Case, Kyle A ; Omolo, Morrine A ; Reiland, Holly A ; Metz, Zachary P ; Diao, Xinyu ; Baumler, David J</creatorcontrib><description>Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0149423</identifier><identifier>PMID: 26885654</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biological evolution ; Biology and Life Sciences ; Computational biology ; Computer and Information Sciences ; Computer applications ; Computer Simulation ; E coli ; Enterobacteriaceae - genetics ; Enterobacteriaceae - growth & development ; Environmental conditions ; Escherichia coli ; Evolution ; Food science ; Genes ; Genes, Bacterial ; Genetic aspects ; Genome, Bacterial ; Genomes ; Genomics ; Genotypes ; Host-bacteria relationships ; Host-Pathogen Interactions - genetics ; Human body ; Humans ; Identification and classification ; Infections ; Linear programming ; Macrophages ; Medicine and Health Sciences ; Metabolism ; Metabolites ; Metabolome - genetics ; Methods ; Microorganisms ; Nutrition ; Organisms ; Predictions ; Salmonella ; Salmonella - genetics ; Simulation ; Strains (organisms) ; Urinary tract ; Urogenital system</subject><ispartof>PloS one, 2016-02, Vol.11 (2), p.e0149423-e0149423</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Ding et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Ding et al 2016 Ding et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c585t-7c50c2ef19e5600388250d49597c341629a9666edc497548a940cf3a2dffea123</citedby><cites>FETCH-LOGICAL-c585t-7c50c2ef19e5600388250d49597c341629a9666edc497548a940cf3a2dffea123</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757543/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4757543/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79569,79570</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26885654$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ding, Tong</creatorcontrib><creatorcontrib>Case, Kyle A</creatorcontrib><creatorcontrib>Omolo, Morrine A</creatorcontrib><creatorcontrib>Reiland, Holly A</creatorcontrib><creatorcontrib>Metz, Zachary P</creatorcontrib><creatorcontrib>Diao, Xinyu</creatorcontrib><creatorcontrib>Baumler, David J</creatorcontrib><title>Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes.</description><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Computational biology</subject><subject>Computer and Information Sciences</subject><subject>Computer applications</subject><subject>Computer Simulation</subject><subject>E coli</subject><subject>Enterobacteriaceae - genetics</subject><subject>Enterobacteriaceae - growth & development</subject><subject>Environmental conditions</subject><subject>Escherichia coli</subject><subject>Evolution</subject><subject>Food science</subject><subject>Genes</subject><subject>Genes, Bacterial</subject><subject>Genetic aspects</subject><subject>Genome, Bacterial</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotypes</subject><subject>Host-bacteria relationships</subject><subject>Host-Pathogen Interactions - genetics</subject><subject>Human body</subject><subject>Humans</subject><subject>Identification and classification</subject><subject>Infections</subject><subject>Linear programming</subject><subject>Macrophages</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Metabolome - genetics</subject><subject>Methods</subject><subject>Microorganisms</subject><subject>Nutrition</subject><subject>Organisms</subject><subject>Predictions</subject><subject>Salmonella</subject><subject>Salmonella - genetics</subject><subject>Simulation</subject><subject>Strains (organisms)</subject><subject>Urinary tract</subject><subject>Urogenital system</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptkt1qFDEUgAdRbK2-geiAIN7smv9MboSyrN1C1UL1OmQzmd2UTLJNMgVfwOc2052WXfEqYc53vnNO5lTVWwjmEHP4-TYM0Ss33wVv5gASQRB-Vp1CgdGMIYCfH9xPqlcp3QJAccPYy-oEsaahjJLT6s91NK3V2fpNvUzJ-GyVq7-ZrNbBWV1fGB96Uy-CzyVWh67-bvXWzG52RtuuAMsSiGGtdDnG1NXQK19fq7wNG-NT3Q5xdN_YfnAq2-BHxyqkXDLvbQy-L970unrRKZfMm-k8q359Xf5crGZXPy4uF-dXM00bmmdcU6CR6aAwlAGAmwZR0BJBBdeYQIaEEowx02oiOCWNEgToDivUdp1REOGz6v3eu3MhyekJk4ScUQEhQLQQl3uiDepW7qLtVfwtg7Ly4UOIG6littoZ2XAKmjXXoGGo1OKCQ0p1qzXoAGCcFNeXqdqw7ktTZdKo3JH0OOLtVm7CvSSclvZxEXyaBDHcDSZl2dukjXPKmzA89M0Bx5TBgn74B_3_dBO1UWUA67tQ6upRKs8JwRQCwseyHw-orVEub1Nww_j70jFI9qCOIaVouqfZIJDjlj42IcctldOWlrR3h-_ylPS4lvgvCh_koQ</recordid><startdate>20160217</startdate><enddate>20160217</enddate><creator>Ding, Tong</creator><creator>Case, Kyle A</creator><creator>Omolo, Morrine A</creator><creator>Reiland, Holly A</creator><creator>Metz, Zachary P</creator><creator>Diao, Xinyu</creator><creator>Baumler, David J</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PHGZM</scope><scope>PHGZT</scope><scope>PIMPY</scope><scope>PJZUB</scope><scope>PKEHL</scope><scope>PPXIY</scope><scope>PQEST</scope><scope>PQGLB</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20160217</creationdate><title>Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments</title><author>Ding, Tong ; Case, Kyle A ; Omolo, Morrine A ; Reiland, Holly A ; Metz, Zachary P ; Diao, Xinyu ; Baumler, David J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c585t-7c50c2ef19e5600388250d49597c341629a9666edc497548a940cf3a2dffea123</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Computational biology</topic><topic>Computer and Information Sciences</topic><topic>Computer applications</topic><topic>Computer Simulation</topic><topic>E coli</topic><topic>Enterobacteriaceae - genetics</topic><topic>Enterobacteriaceae - growth & development</topic><topic>Environmental conditions</topic><topic>Escherichia coli</topic><topic>Evolution</topic><topic>Food science</topic><topic>Genes</topic><topic>Genes, Bacterial</topic><topic>Genetic aspects</topic><topic>Genome, Bacterial</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotypes</topic><topic>Host-bacteria relationships</topic><topic>Host-Pathogen Interactions - genetics</topic><topic>Human body</topic><topic>Humans</topic><topic>Identification and classification</topic><topic>Infections</topic><topic>Linear programming</topic><topic>Macrophages</topic><topic>Medicine and Health Sciences</topic><topic>Metabolism</topic><topic>Metabolites</topic><topic>Metabolome - genetics</topic><topic>Methods</topic><topic>Microorganisms</topic><topic>Nutrition</topic><topic>Organisms</topic><topic>Predictions</topic><topic>Salmonella</topic><topic>Salmonella - genetics</topic><topic>Simulation</topic><topic>Strains (organisms)</topic><topic>Urinary tract</topic><topic>Urogenital system</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ding, Tong</creatorcontrib><creatorcontrib>Case, Kyle A</creatorcontrib><creatorcontrib>Omolo, Morrine A</creatorcontrib><creatorcontrib>Reiland, Holly A</creatorcontrib><creatorcontrib>Metz, Zachary P</creatorcontrib><creatorcontrib>Diao, Xinyu</creatorcontrib><creatorcontrib>Baumler, David J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>ProQuest Central (New)</collection><collection>ProQuest One Academic (New)</collection><collection>Publicly Available Content Database</collection><collection>ProQuest Health & Medical Research Collection</collection><collection>ProQuest One Academic Middle East (New)</collection><collection>ProQuest One Health & Nursing</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Applied & Life Sciences</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ding, Tong</au><au>Case, Kyle A</au><au>Omolo, Morrine A</au><au>Reiland, Holly A</au><au>Metz, Zachary P</au><au>Diao, Xinyu</au><au>Baumler, David J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-02-17</date><risdate>2016</risdate><volume>11</volume><issue>2</issue><spage>e0149423</spage><epage>e0149423</epage><pages>e0149423-e0149423</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26885654</pmid><doi>10.1371/journal.pone.0149423</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2016-02, Vol.11 (2), p.e0149423-e0149423 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1765911025 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Biological evolution Biology and Life Sciences Computational biology Computer and Information Sciences Computer applications Computer Simulation E coli Enterobacteriaceae - genetics Enterobacteriaceae - growth & development Environmental conditions Escherichia coli Evolution Food science Genes Genes, Bacterial Genetic aspects Genome, Bacterial Genomes Genomics Genotypes Host-bacteria relationships Host-Pathogen Interactions - genetics Human body Humans Identification and classification Infections Linear programming Macrophages Medicine and Health Sciences Metabolism Metabolites Metabolome - genetics Methods Microorganisms Nutrition Organisms Predictions Salmonella Salmonella - genetics Simulation Strains (organisms) Urinary tract Urogenital system |
| title | Predicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-21T18%3A40%3A33IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Predicting%20Essential%20Metabolic%20Genome%20Content%20of%20Niche-Specific%20Enterobacterial%20Human%20Pathogens%20during%20Simulation%20of%20Host%20Environments&rft.jtitle=PloS%20one&rft.au=Ding,%20Tong&rft.date=2016-02-17&rft.volume=11&rft.issue=2&rft.spage=e0149423&rft.epage=e0149423&rft.pages=e0149423-e0149423&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0149423&rft_dat=%3Cgale_plos_%3EA443510473%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1765911025&rft_id=info:pmid/26885654&rft_galeid=A443510473&rft_doaj_id=oai_doaj_org_article_87508b7c086248a797155cdcc0f00674&rfr_iscdi=true |