Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism

Autores
Mohamed, María Florencia; Ordoñez, Omar Federico; Raya, Raul Ricardo; Mozzi, Fernanda Beatriz
Año de publicación
2021
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
The Fructobacillus genus is a group of obligatory fructophilic lactic acid bacteria, recently reclassified from Leuconostoc due to phylogenetic and biochemical differences. These bacteria require the use of fructose or another electron acceptor for its growth, because of the lack of an alcohol-acetaldehyde dehydrogenase gene (adhE). Previously, some genomic differences were reported in Fructobacillus respect to Leuconostoc, suggesting a reductive evolution in carbohydrate metabolism caused by an adaptation to fructose-rich niches. In this work, we performed a comparative genomic analysis in the genus Fructobacillus to evaluate possible genomic and metabolic differences among species. For this, nine Fructobacillus genomes were used. As expected, the GC content was highly similar among this genus (43,9 ? 44,8 %mol); however, some differences were found in genome size and number of CDS being the genomes of F. durionis DSM 19113 and F. sp. CRL 2054 smaller (1,32 Mb) than F. tropaeoli genomes (1,66 ? 1,68 Mb). Six intact prophage regions (20,6 ? 30,5 kb) were identified in four strains whereas Type II CRISPR-Cas systems were found in five genomes. A bacteriocin-coding gene was only found in F. durionis DSM 19113. Plasmids and antibiotic resistance genes were not detected in the studied genomes. Phylogenetic analyses were done based on 16S rRNA sequences and Fructobacillus core-genome. Both phylogenetic trees allowed us to distinguish two different phylogroups in this genus. Phylogroup 1 was composed by F. sp. CRL 2054, F. durionis and F. fructosus strains, whereas F. ficulneus, F. pseudoficulneus, F. sp. EFB-N1 and F. tropaeoli strains formed part of phylogroup 2. A pangenome analysis showed important differences in presence/absence of genes between both groups. Consequently, annotation of genomes in COG and KEGG databases was performed to classify genes according to its metabolic function. The number of genes involved in COG categories E, F, H and P related with metabolism were significantly lower (p<0,05) in phylogroup 1. This group of strains also presented an important decrease in the number of genes involved in synthesis of five amino acids, when comparing to phylogroup 2 and L. mesenteroides ATCC 8293. This reduction in the amino acid metabolism was also observed experimentally in F. sp. CRL 2054 and F. tropaeoli CRL 2034. Finally, the presence of genes involved in central carbohydrate metabolism was evaluated among the strains. Differences were detected in genes related to fructose metabolism (fk, gpi) and genes related to the use of electron acceptors (D- and L- ldh, adh, budC, yjlD); however, those variations were not always related to the phylogeny between organisms. In conclusion, two groups with important genomic differences were identified in Fructobacillus; moreover, the presence of genes involved in NADH reoxidation and fructose intake was variable throughout the genus.
Fil: Mohamed, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Ordoñez, Omar Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina
Fil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Mozzi, Fernanda Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology
Mendoza
Argentina
Sociedad Argentina de Investigación en Bioquímica y Biología Molecular
Sociedad Argentina de Microbiología General
Materia
COMPARATIVE GENOMICS
FRUCTOBACILLUS
FRUCTOPHILIC LACTIC ACID BACTERIA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/193425

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network_name_str CONICET Digital (CONICET)
spelling Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolismMohamed, María FlorenciaOrdoñez, Omar FedericoRaya, Raul RicardoMozzi, Fernanda BeatrizCOMPARATIVE GENOMICSFRUCTOBACILLUSFRUCTOPHILIC LACTIC ACID BACTERIAhttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1The Fructobacillus genus is a group of obligatory fructophilic lactic acid bacteria, recently reclassified from Leuconostoc due to phylogenetic and biochemical differences. These bacteria require the use of fructose or another electron acceptor for its growth, because of the lack of an alcohol-acetaldehyde dehydrogenase gene (adhE). Previously, some genomic differences were reported in Fructobacillus respect to Leuconostoc, suggesting a reductive evolution in carbohydrate metabolism caused by an adaptation to fructose-rich niches. In this work, we performed a comparative genomic analysis in the genus Fructobacillus to evaluate possible genomic and metabolic differences among species. For this, nine Fructobacillus genomes were used. As expected, the GC content was highly similar among this genus (43,9 ? 44,8 %mol); however, some differences were found in genome size and number of CDS being the genomes of F. durionis DSM 19113 and F. sp. CRL 2054 smaller (1,32 Mb) than F. tropaeoli genomes (1,66 ? 1,68 Mb). Six intact prophage regions (20,6 ? 30,5 kb) were identified in four strains whereas Type II CRISPR-Cas systems were found in five genomes. A bacteriocin-coding gene was only found in F. durionis DSM 19113. Plasmids and antibiotic resistance genes were not detected in the studied genomes. Phylogenetic analyses were done based on 16S rRNA sequences and Fructobacillus core-genome. Both phylogenetic trees allowed us to distinguish two different phylogroups in this genus. Phylogroup 1 was composed by F. sp. CRL 2054, F. durionis and F. fructosus strains, whereas F. ficulneus, F. pseudoficulneus, F. sp. EFB-N1 and F. tropaeoli strains formed part of phylogroup 2. A pangenome analysis showed important differences in presence/absence of genes between both groups. Consequently, annotation of genomes in COG and KEGG databases was performed to classify genes according to its metabolic function. The number of genes involved in COG categories E, F, H and P related with metabolism were significantly lower (p<0,05) in phylogroup 1. This group of strains also presented an important decrease in the number of genes involved in synthesis of five amino acids, when comparing to phylogroup 2 and L. mesenteroides ATCC 8293. This reduction in the amino acid metabolism was also observed experimentally in F. sp. CRL 2054 and F. tropaeoli CRL 2034. Finally, the presence of genes involved in central carbohydrate metabolism was evaluated among the strains. Differences were detected in genes related to fructose metabolism (fk, gpi) and genes related to the use of electron acceptors (D- and L- ldh, adh, budC, yjlD); however, those variations were not always related to the phylogeny between organisms. In conclusion, two groups with important genomic differences were identified in Fructobacillus; moreover, the presence of genes involved in NADH reoxidation and fructose intake was variable throughout the genus.Fil: Mohamed, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Ordoñez, Omar Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Centro de Investigación y Extensión Forestal Andino Patagónico; ArgentinaFil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaFil: Mozzi, Fernanda Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; ArgentinaLVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General MicrobiologyMendozaArgentinaSociedad Argentina de Investigación en Bioquímica y Biología MolecularSociedad Argentina de Microbiología GeneralTech Science Press2021info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectReuniónJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/193425Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; Mendoza; Argentina; 2020; 54-540327-95451667-5746CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.techscience.com/biocell/v45nSuppl.1/42376Nacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:36:37Zoai:ri.conicet.gov.ar:11336/193425instacron: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 09:36:37.638CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
title Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
spellingShingle Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
Mohamed, María Florencia
COMPARATIVE GENOMICS
FRUCTOBACILLUS
FRUCTOPHILIC LACTIC ACID BACTERIA
title_short Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
title_full Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
title_fullStr Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
title_full_unstemmed Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
title_sort Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism
dc.creator.none.fl_str_mv Mohamed, María Florencia
Ordoñez, Omar Federico
Raya, Raul Ricardo
Mozzi, Fernanda Beatriz
author Mohamed, María Florencia
author_facet Mohamed, María Florencia
Ordoñez, Omar Federico
Raya, Raul Ricardo
Mozzi, Fernanda Beatriz
author_role author
author2 Ordoñez, Omar Federico
Raya, Raul Ricardo
Mozzi, Fernanda Beatriz
author2_role author
author
author
dc.subject.none.fl_str_mv COMPARATIVE GENOMICS
FRUCTOBACILLUS
FRUCTOPHILIC LACTIC ACID BACTERIA
topic COMPARATIVE GENOMICS
FRUCTOBACILLUS
FRUCTOPHILIC LACTIC ACID BACTERIA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.2
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The Fructobacillus genus is a group of obligatory fructophilic lactic acid bacteria, recently reclassified from Leuconostoc due to phylogenetic and biochemical differences. These bacteria require the use of fructose or another electron acceptor for its growth, because of the lack of an alcohol-acetaldehyde dehydrogenase gene (adhE). Previously, some genomic differences were reported in Fructobacillus respect to Leuconostoc, suggesting a reductive evolution in carbohydrate metabolism caused by an adaptation to fructose-rich niches. In this work, we performed a comparative genomic analysis in the genus Fructobacillus to evaluate possible genomic and metabolic differences among species. For this, nine Fructobacillus genomes were used. As expected, the GC content was highly similar among this genus (43,9 ? 44,8 %mol); however, some differences were found in genome size and number of CDS being the genomes of F. durionis DSM 19113 and F. sp. CRL 2054 smaller (1,32 Mb) than F. tropaeoli genomes (1,66 ? 1,68 Mb). Six intact prophage regions (20,6 ? 30,5 kb) were identified in four strains whereas Type II CRISPR-Cas systems were found in five genomes. A bacteriocin-coding gene was only found in F. durionis DSM 19113. Plasmids and antibiotic resistance genes were not detected in the studied genomes. Phylogenetic analyses were done based on 16S rRNA sequences and Fructobacillus core-genome. Both phylogenetic trees allowed us to distinguish two different phylogroups in this genus. Phylogroup 1 was composed by F. sp. CRL 2054, F. durionis and F. fructosus strains, whereas F. ficulneus, F. pseudoficulneus, F. sp. EFB-N1 and F. tropaeoli strains formed part of phylogroup 2. A pangenome analysis showed important differences in presence/absence of genes between both groups. Consequently, annotation of genomes in COG and KEGG databases was performed to classify genes according to its metabolic function. The number of genes involved in COG categories E, F, H and P related with metabolism were significantly lower (p<0,05) in phylogroup 1. This group of strains also presented an important decrease in the number of genes involved in synthesis of five amino acids, when comparing to phylogroup 2 and L. mesenteroides ATCC 8293. This reduction in the amino acid metabolism was also observed experimentally in F. sp. CRL 2054 and F. tropaeoli CRL 2034. Finally, the presence of genes involved in central carbohydrate metabolism was evaluated among the strains. Differences were detected in genes related to fructose metabolism (fk, gpi) and genes related to the use of electron acceptors (D- and L- ldh, adh, budC, yjlD); however, those variations were not always related to the phylogeny between organisms. In conclusion, two groups with important genomic differences were identified in Fructobacillus; moreover, the presence of genes involved in NADH reoxidation and fructose intake was variable throughout the genus.
Fil: Mohamed, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Ordoñez, Omar Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Centro de Investigación y Extensión Forestal Andino Patagónico; Argentina
Fil: Raya, Raul Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
Fil: Mozzi, Fernanda Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina
LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology
Mendoza
Argentina
Sociedad Argentina de Investigación en Bioquímica y Biología Molecular
Sociedad Argentina de Microbiología General
description The Fructobacillus genus is a group of obligatory fructophilic lactic acid bacteria, recently reclassified from Leuconostoc due to phylogenetic and biochemical differences. These bacteria require the use of fructose or another electron acceptor for its growth, because of the lack of an alcohol-acetaldehyde dehydrogenase gene (adhE). Previously, some genomic differences were reported in Fructobacillus respect to Leuconostoc, suggesting a reductive evolution in carbohydrate metabolism caused by an adaptation to fructose-rich niches. In this work, we performed a comparative genomic analysis in the genus Fructobacillus to evaluate possible genomic and metabolic differences among species. For this, nine Fructobacillus genomes were used. As expected, the GC content was highly similar among this genus (43,9 ? 44,8 %mol); however, some differences were found in genome size and number of CDS being the genomes of F. durionis DSM 19113 and F. sp. CRL 2054 smaller (1,32 Mb) than F. tropaeoli genomes (1,66 ? 1,68 Mb). Six intact prophage regions (20,6 ? 30,5 kb) were identified in four strains whereas Type II CRISPR-Cas systems were found in five genomes. A bacteriocin-coding gene was only found in F. durionis DSM 19113. Plasmids and antibiotic resistance genes were not detected in the studied genomes. Phylogenetic analyses were done based on 16S rRNA sequences and Fructobacillus core-genome. Both phylogenetic trees allowed us to distinguish two different phylogroups in this genus. Phylogroup 1 was composed by F. sp. CRL 2054, F. durionis and F. fructosus strains, whereas F. ficulneus, F. pseudoficulneus, F. sp. EFB-N1 and F. tropaeoli strains formed part of phylogroup 2. A pangenome analysis showed important differences in presence/absence of genes between both groups. Consequently, annotation of genomes in COG and KEGG databases was performed to classify genes according to its metabolic function. The number of genes involved in COG categories E, F, H and P related with metabolism were significantly lower (p<0,05) in phylogroup 1. This group of strains also presented an important decrease in the number of genes involved in synthesis of five amino acids, when comparing to phylogroup 2 and L. mesenteroides ATCC 8293. This reduction in the amino acid metabolism was also observed experimentally in F. sp. CRL 2054 and F. tropaeoli CRL 2034. Finally, the presence of genes involved in central carbohydrate metabolism was evaluated among the strains. Differences were detected in genes related to fructose metabolism (fk, gpi) and genes related to the use of electron acceptors (D- and L- ldh, adh, budC, yjlD); however, those variations were not always related to the phylogeny between organisms. In conclusion, two groups with important genomic differences were identified in Fructobacillus; moreover, the presence of genes involved in NADH reoxidation and fructose intake was variable throughout the genus.
publishDate 2021
dc.date.none.fl_str_mv 2021
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dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/193425
Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; Mendoza; Argentina; 2020; 54-54
0327-9545
1667-5746
CONICET Digital
CONICET
url http://hdl.handle.net/11336/193425
identifier_str_mv Comparative genomic analysis of the Fructobacillus genus reveals important differences in amino acid metabolism; LVI Annual Meeting Argentine Society for Biochemistry and Molecular Biology; XV Annual Meeting Argentinean Society for General Microbiology; Mendoza; Argentina; 2020; 54-54
0327-9545
1667-5746
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
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