Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei
Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% vari...
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description | Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products. |
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A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.</description><identifier>ISSN: 0099-2240</identifier><identifier>EISSN: 1098-5336</identifier><identifier>EISSN: 1098-6596</identifier><identifier>DOI: 10.1128/AEM.01721-08</identifier><identifier>PMID: 19114527</identifier><identifier>CODEN: AEMIDF</identifier><language>eng</language><publisher>Washington, DC: American Society for Microbiology</publisher><subject>Adaptations ; Bacteria ; Bacterial Proteins - analysis ; Biological and medical sciences ; Biological variation ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial - chemistry ; DNA, Bacterial - genetics ; Electrophoresis, Gel, Pulsed-Field ; Evolutionary and Genomic Microbiology ; Fish Products - microbiology ; Fundamental and applied biological sciences. Psychology ; Genetic diversity ; Genetics ; Genomics ; Genotype ; Genotype & phenotype ; Lactobacillus - chemistry ; Lactobacillus - classification ; Lactobacillus - genetics ; Lactobacillus - isolation & purification ; Life Sciences ; Meat Products - microbiology ; Microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Proteome ; Sequence Analysis, DNA</subject><ispartof>Applied and Environmental Microbiology, 2009-02, Vol.75 (4), p.970-980</ispartof><rights>2009 INIST-CNRS</rights><rights>Copyright American Society for Microbiology Feb 2009</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>Copyright © 2009, American Society for Microbiology</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c553t-10a662943733ff22d604e93f611402dfd778c656de9843817fd73c3c704610f83</citedby><cites>FETCH-LOGICAL-c553t-10a662943733ff22d604e93f611402dfd778c656de9843817fd73c3c704610f83</cites><orcidid>0000-0003-2229-0697 ; 0000-0001-7320-538X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643555/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2643555/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,3188,3189,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21139840$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19114527$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-01190024$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Chaillou, Stéphane</creatorcontrib><creatorcontrib>Daty, Marie</creatorcontrib><creatorcontrib>Baraige, Fabienne</creatorcontrib><creatorcontrib>Dudez, Anne-Marie</creatorcontrib><creatorcontrib>Anglade, Patricia</creatorcontrib><creatorcontrib>Jones, Rhys</creatorcontrib><creatorcontrib>Alpert, Carl-Alfred</creatorcontrib><creatorcontrib>Champomier-Vergès, Marie-Christine</creatorcontrib><creatorcontrib>Zagorec, Monique</creatorcontrib><title>Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei</title><title>Applied and Environmental Microbiology</title><addtitle>Appl Environ Microbiol</addtitle><description>Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.</description><subject>Adaptations</subject><subject>Bacteria</subject><subject>Bacterial Proteins - analysis</subject><subject>Biological and medical sciences</subject><subject>Biological variation</subject><subject>Cluster Analysis</subject><subject>DNA Fingerprinting</subject><subject>DNA, Bacterial - chemistry</subject><subject>DNA, Bacterial - genetics</subject><subject>Electrophoresis, Gel, Pulsed-Field</subject><subject>Evolutionary and Genomic Microbiology</subject><subject>Fish Products - microbiology</subject><subject>Fundamental and applied biological sciences. 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Psychology</topic><topic>Genetic diversity</topic><topic>Genetics</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotype & phenotype</topic><topic>Lactobacillus - chemistry</topic><topic>Lactobacillus - classification</topic><topic>Lactobacillus - genetics</topic><topic>Lactobacillus - isolation & purification</topic><topic>Life Sciences</topic><topic>Meat Products - microbiology</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>Polymorphism, Genetic</topic><topic>Proteome</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chaillou, Stéphane</creatorcontrib><creatorcontrib>Daty, Marie</creatorcontrib><creatorcontrib>Baraige, Fabienne</creatorcontrib><creatorcontrib>Dudez, Anne-Marie</creatorcontrib><creatorcontrib>Anglade, Patricia</creatorcontrib><creatorcontrib>Jones, Rhys</creatorcontrib><creatorcontrib>Alpert, Carl-Alfred</creatorcontrib><creatorcontrib>Champomier-Vergès, Marie-Christine</creatorcontrib><creatorcontrib>Zagorec, Monique</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Applied and Environmental Microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chaillou, Stéphane</au><au>Daty, Marie</au><au>Baraige, Fabienne</au><au>Dudez, Anne-Marie</au><au>Anglade, Patricia</au><au>Jones, Rhys</au><au>Alpert, Carl-Alfred</au><au>Champomier-Vergès, Marie-Christine</au><au>Zagorec, Monique</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei</atitle><jtitle>Applied and Environmental Microbiology</jtitle><addtitle>Appl Environ Microbiol</addtitle><date>2009-02</date><risdate>2009</risdate><volume>75</volume><issue>4</issue><spage>970</spage><epage>980</epage><pages>970-980</pages><issn>0099-2240</issn><eissn>1098-5336</eissn><eissn>1098-6596</eissn><coden>AEMIDF</coden><abstract>Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.</abstract><cop>Washington, DC</cop><pub>American Society for Microbiology</pub><pmid>19114527</pmid><doi>10.1128/AEM.01721-08</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0003-2229-0697</orcidid><orcidid>https://orcid.org/0000-0001-7320-538X</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Adaptations Bacteria Bacterial Proteins - analysis Biological and medical sciences Biological variation Cluster Analysis DNA Fingerprinting DNA, Bacterial - chemistry DNA, Bacterial - genetics Electrophoresis, Gel, Pulsed-Field Evolutionary and Genomic Microbiology Fish Products - microbiology Fundamental and applied biological sciences. Psychology Genetic diversity Genetics Genomics Genotype Genotype & phenotype Lactobacillus - chemistry Lactobacillus - classification Lactobacillus - genetics Lactobacillus - isolation & purification Life Sciences Meat Products - microbiology Microbiology Molecular Sequence Data Phylogeny Polymerase Chain Reaction Polymorphism, Genetic Proteome Sequence Analysis, DNA |
title | Intraspecies Genomic Diversity and Natural Population Structure of the Meat-Borne Lactic Acid Bacterium Lactobacillus sakei |
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