Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates

Autores
Teran, Lucrecia Cecilia; Coeuret, Gwendoline; Raya, Raul Ricardo; Zagorec, Monique; Champomier-Vergès, Marie-Christine; Chaillou, Stéphane
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
Fil: Teran, Lucrecia Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Coeuret, Gwendoline. Institut National de la Recherche Agronomique; Francia
Fil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Zagorec, Monique. Institut National de la Recherche Agronomique; Francia
Fil: Champomier-Vergès, Marie-Christine. Institut National de la Recherche Agronomique; Francia
Fil: Chaillou, Stéphane. Institut National de la Recherche Agronomique; Francia
Materia
PANGENOME
LACTOBACILLUS CURVATUS
PLANT FERMENTATION
FOOD
LACTIC ACID BACTERIA
PHYLOGENOMICS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/81532

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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydratesTeran, Lucrecia CeciliaCoeuret, GwendolineRaya, Raul RicardoZagorec, MoniqueChampomier-Vergès, Marie-ChristineChaillou, StéphanePANGENOMELACTOBACILLUS CURVATUSPLANT FERMENTATIONFOODLACTIC ACID BACTERIAPHYLOGENOMICShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1https://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.Fil: Teran, Lucrecia Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Coeuret, Gwendoline. Institut National de la Recherche Agronomique; FranciaFil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Zagorec, Monique. Institut National de la Recherche Agronomique; FranciaFil: Champomier-Vergès, Marie-Christine. Institut National de la Recherche Agronomique; FranciaFil: Chaillou, Stéphane. Institut National de la Recherche Agronomique; FranciaOxford University Press2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/81532Teran, Lucrecia Cecilia; Coeuret, Gwendoline; Raya, Raul Ricardo; Zagorec, Monique; Champomier-Vergès, Marie-Christine; et al.; Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates; Oxford University Press; Genome Biology and Evolution; 10; 6; 6-2018; 1516-15251759-6653CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evy106info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gbe/article/10/6/1516/5020733info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:40:19Zoai:ri.conicet.gov.ar:11336/81532instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:40:19.64CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
title Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
spellingShingle Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
Teran, Lucrecia Cecilia
PANGENOME
LACTOBACILLUS CURVATUS
PLANT FERMENTATION
FOOD
LACTIC ACID BACTERIA
PHYLOGENOMICS
title_short Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
title_full Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
title_fullStr Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
title_full_unstemmed Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
title_sort Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates
dc.creator.none.fl_str_mv Teran, Lucrecia Cecilia
Coeuret, Gwendoline
Raya, Raul Ricardo
Zagorec, Monique
Champomier-Vergès, Marie-Christine
Chaillou, Stéphane
author Teran, Lucrecia Cecilia
author_facet Teran, Lucrecia Cecilia
Coeuret, Gwendoline
Raya, Raul Ricardo
Zagorec, Monique
Champomier-Vergès, Marie-Christine
Chaillou, Stéphane
author_role author
author2 Coeuret, Gwendoline
Raya, Raul Ricardo
Zagorec, Monique
Champomier-Vergès, Marie-Christine
Chaillou, Stéphane
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv PANGENOME
LACTOBACILLUS CURVATUS
PLANT FERMENTATION
FOOD
LACTIC ACID BACTERIA
PHYLOGENOMICS
topic PANGENOME
LACTOBACILLUS CURVATUS
PLANT FERMENTATION
FOOD
LACTIC ACID BACTERIA
PHYLOGENOMICS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
Fil: Teran, Lucrecia Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Coeuret, Gwendoline. Institut National de la Recherche Agronomique; Francia
Fil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Zagorec, Monique. Institut National de la Recherche Agronomique; Francia
Fil: Champomier-Vergès, Marie-Christine. Institut National de la Recherche Agronomique; Francia
Fil: Chaillou, Stéphane. Institut National de la Recherche Agronomique; Francia
description Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.
publishDate 2018
dc.date.none.fl_str_mv 2018-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/81532
Teran, Lucrecia Cecilia; Coeuret, Gwendoline; Raya, Raul Ricardo; Zagorec, Monique; Champomier-Vergès, Marie-Christine; et al.; Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates; Oxford University Press; Genome Biology and Evolution; 10; 6; 6-2018; 1516-1525
1759-6653
CONICET Digital
CONICET
url http://hdl.handle.net/11336/81532
identifier_str_mv Teran, Lucrecia Cecilia; Coeuret, Gwendoline; Raya, Raul Ricardo; Zagorec, Monique; Champomier-Vergès, Marie-Christine; et al.; Phylogenomic analysis of lactobacillus curvatus reveals two lineages distinguished by genes for fermenting plant-derived carbohydrates; Oxford University Press; Genome Biology and Evolution; 10; 6; 6-2018; 1516-1525
1759-6653
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evy106
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/gbe/article/10/6/1516/5020733
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
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instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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