Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights

Autores
Medina Canalejo, Luis M.; Ruiz, María Julia; Martín Gómez, Andrés; Chiesa, Francesco; Rubiola, Selene; Novara, Giulia; Arce, Lourdes
Año de publicación
2024
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
The production of dry-cured ham, with roots tracing back to ancient recipes, grapples with persistent technological challenges, resulting in defects and financial setbacks. Traditionally, the identification of microbial defects relies on the "probe and sniff technique" conducted approximately between the 10th and 12th month of aging. These potential defects, broadly classified into deep spoilage and surface defects, pose a significant hurdle for the ham industry.In this comprehensive study, we sampled and analyzed three defective dry-cured hams, exhibiting noticeable defects, and three normal hams carefully chosen from a producer in Andalusia, Spain. The objective was to scrutinize the microbiome of these samples to understand whether the observed defects were associated with shifts in the microbial population.16s multi-amplicon sequencing was performed using the Ion 16S Metagenomics Kit and Ion Torrent Sequencing Platform. Raw reads were then analysed using QIIME2 for data processing. Alpha-diversity and beta-diversity indexes, ANCOM test, Linear Discriminant Analysis (LEfSe) and co-occurrence network analysis were computed and visualized using the “microeco” R package.A pangenomic analysis and functional enrichment analysis of genomes available in the NCBI database was conducted.The analysis unveiled a distinctive association between Tetragenococcus, a genus recognized for its prevalence in fermented fish and vegetable products, as well as in cheese microbiota, and defective dry-cured hams. Both the LEfSe and ANCOM tests concurred in highlighting this taxon as a potential culprit.Subsequent scrutiny of Tetragenococcus genomes highlighted disparities between the two species T. koreensis and T. halophilus in terms of metabolic activity. Notably, T. koreensis manifested a distinctive set of genes encoding enzymes for carbohydrate metabolism. This study not only provided the opportunity to address the producer´s inquiry regarding the potential role of a specific microbial population in causing the defect, but also indicated the likelihood of a halotolerant microorganism being the culprit.While previous research has linked halotolerant microorganisms to defects in dry-cured meat, this represents the first time Tetragenococcus has been linked to such cases. This result sheds light on Tetragenococcus´ involvement in defected dry-cured hams.Ongoing investigations will focus on identifying the specific Tetragenococcus strains responsible for these defects, helping to refine our knowledge of their impact on dry-cured ham production.
Fil: Medina Canalejo, Luis M.. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; España
Fil: Ruiz, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina
Fil: Martín Gómez, Andrés. Cooperativa Ganadera del Valle de los Pedroches; España
Fil: Chiesa, Francesco. Università di Torino; Italia
Fil: Rubiola, Selene. Università di Torino; Italia
Fil: Novara, Giulia. Università di Torino; Italia
Fil: Arce, Lourdes. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; España
28th International Conference on Food Microbiology and Hygiene
Burgos
España
International Committee on Food Microbiology and Hygiene
Materia
TETRAGENOCOCCUS
DRY CURED HAM
MICOBIOME ANALYSIS
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:11336/257507

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network_name_str CONICET Digital (CONICET)
spelling Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insightsMedina Canalejo, Luis M.Ruiz, María JuliaMartín Gómez, AndrésChiesa, FrancescoRubiola, SeleneNovara, GiuliaArce, LourdesTETRAGENOCOCCUSDRY CURED HAMMICOBIOME ANALYSIShttps://purl.org/becyt/ford/4.3https://purl.org/becyt/ford/4The production of dry-cured ham, with roots tracing back to ancient recipes, grapples with persistent technological challenges, resulting in defects and financial setbacks. Traditionally, the identification of microbial defects relies on the "probe and sniff technique" conducted approximately between the 10th and 12th month of aging. These potential defects, broadly classified into deep spoilage and surface defects, pose a significant hurdle for the ham industry.In this comprehensive study, we sampled and analyzed three defective dry-cured hams, exhibiting noticeable defects, and three normal hams carefully chosen from a producer in Andalusia, Spain. The objective was to scrutinize the microbiome of these samples to understand whether the observed defects were associated with shifts in the microbial population.16s multi-amplicon sequencing was performed using the Ion 16S Metagenomics Kit and Ion Torrent Sequencing Platform. Raw reads were then analysed using QIIME2 for data processing. Alpha-diversity and beta-diversity indexes, ANCOM test, Linear Discriminant Analysis (LEfSe) and co-occurrence network analysis were computed and visualized using the “microeco” R package.A pangenomic analysis and functional enrichment analysis of genomes available in the NCBI database was conducted.The analysis unveiled a distinctive association between Tetragenococcus, a genus recognized for its prevalence in fermented fish and vegetable products, as well as in cheese microbiota, and defective dry-cured hams. Both the LEfSe and ANCOM tests concurred in highlighting this taxon as a potential culprit.Subsequent scrutiny of Tetragenococcus genomes highlighted disparities between the two species T. koreensis and T. halophilus in terms of metabolic activity. Notably, T. koreensis manifested a distinctive set of genes encoding enzymes for carbohydrate metabolism. This study not only provided the opportunity to address the producer´s inquiry regarding the potential role of a specific microbial population in causing the defect, but also indicated the likelihood of a halotolerant microorganism being the culprit.While previous research has linked halotolerant microorganisms to defects in dry-cured meat, this represents the first time Tetragenococcus has been linked to such cases. This result sheds light on Tetragenococcus´ involvement in defected dry-cured hams.Ongoing investigations will focus on identifying the specific Tetragenococcus strains responsible for these defects, helping to refine our knowledge of their impact on dry-cured ham production.Fil: Medina Canalejo, Luis M.. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; EspañaFil: Ruiz, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; ArgentinaFil: Martín Gómez, Andrés. Cooperativa Ganadera del Valle de los Pedroches; EspañaFil: Chiesa, Francesco. Università di Torino; ItaliaFil: Rubiola, Selene. Università di Torino; ItaliaFil: Novara, Giulia. Università di Torino; ItaliaFil: Arce, Lourdes. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; España28th International Conference on Food Microbiology and HygieneBurgosEspañaInternational Committee on Food Microbiology and HygieneInternational Committee on Food Microbiology and Hygiene2024info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/257507Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights; 28th International Conference on Food Microbiology and Hygiene; Burgos; España; 2024; 156-157CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://foodmicro2024.com/ABSTRACT_FOOD_MICRO_2024_V2.pdfInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:06:51Zoai:ri.conicet.gov.ar:11336/257507instacron: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 10:06:52.231CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
title Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
spellingShingle Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
Medina Canalejo, Luis M.
TETRAGENOCOCCUS
DRY CURED HAM
MICOBIOME ANALYSIS
title_short Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
title_full Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
title_fullStr Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
title_full_unstemmed Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
title_sort Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights
dc.creator.none.fl_str_mv Medina Canalejo, Luis M.
Ruiz, María Julia
Martín Gómez, Andrés
Chiesa, Francesco
Rubiola, Selene
Novara, Giulia
Arce, Lourdes
author Medina Canalejo, Luis M.
author_facet Medina Canalejo, Luis M.
Ruiz, María Julia
Martín Gómez, Andrés
Chiesa, Francesco
Rubiola, Selene
Novara, Giulia
Arce, Lourdes
author_role author
author2 Ruiz, María Julia
Martín Gómez, Andrés
Chiesa, Francesco
Rubiola, Selene
Novara, Giulia
Arce, Lourdes
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv TETRAGENOCOCCUS
DRY CURED HAM
MICOBIOME ANALYSIS
topic TETRAGENOCOCCUS
DRY CURED HAM
MICOBIOME ANALYSIS
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.3
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv The production of dry-cured ham, with roots tracing back to ancient recipes, grapples with persistent technological challenges, resulting in defects and financial setbacks. Traditionally, the identification of microbial defects relies on the "probe and sniff technique" conducted approximately between the 10th and 12th month of aging. These potential defects, broadly classified into deep spoilage and surface defects, pose a significant hurdle for the ham industry.In this comprehensive study, we sampled and analyzed three defective dry-cured hams, exhibiting noticeable defects, and three normal hams carefully chosen from a producer in Andalusia, Spain. The objective was to scrutinize the microbiome of these samples to understand whether the observed defects were associated with shifts in the microbial population.16s multi-amplicon sequencing was performed using the Ion 16S Metagenomics Kit and Ion Torrent Sequencing Platform. Raw reads were then analysed using QIIME2 for data processing. Alpha-diversity and beta-diversity indexes, ANCOM test, Linear Discriminant Analysis (LEfSe) and co-occurrence network analysis were computed and visualized using the “microeco” R package.A pangenomic analysis and functional enrichment analysis of genomes available in the NCBI database was conducted.The analysis unveiled a distinctive association between Tetragenococcus, a genus recognized for its prevalence in fermented fish and vegetable products, as well as in cheese microbiota, and defective dry-cured hams. Both the LEfSe and ANCOM tests concurred in highlighting this taxon as a potential culprit.Subsequent scrutiny of Tetragenococcus genomes highlighted disparities between the two species T. koreensis and T. halophilus in terms of metabolic activity. Notably, T. koreensis manifested a distinctive set of genes encoding enzymes for carbohydrate metabolism. This study not only provided the opportunity to address the producer´s inquiry regarding the potential role of a specific microbial population in causing the defect, but also indicated the likelihood of a halotolerant microorganism being the culprit.While previous research has linked halotolerant microorganisms to defects in dry-cured meat, this represents the first time Tetragenococcus has been linked to such cases. This result sheds light on Tetragenococcus´ involvement in defected dry-cured hams.Ongoing investigations will focus on identifying the specific Tetragenococcus strains responsible for these defects, helping to refine our knowledge of their impact on dry-cured ham production.
Fil: Medina Canalejo, Luis M.. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; España
Fil: Ruiz, María Julia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Centro de Investigación Veterinaria de Tandil. Universidad Nacional del Centro de la Provincia de Buenos Aires. Centro de Investigación Veterinaria de Tandil. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Centro de Investigación Veterinaria de Tandil; Argentina
Fil: Martín Gómez, Andrés. Cooperativa Ganadera del Valle de los Pedroches; España
Fil: Chiesa, Francesco. Università di Torino; Italia
Fil: Rubiola, Selene. Università di Torino; Italia
Fil: Novara, Giulia. Università di Torino; Italia
Fil: Arce, Lourdes. Universidad de Córdoba. Instituto Universitario de Investigación en Química Fina y Nanoquímica; España
28th International Conference on Food Microbiology and Hygiene
Burgos
España
International Committee on Food Microbiology and Hygiene
description The production of dry-cured ham, with roots tracing back to ancient recipes, grapples with persistent technological challenges, resulting in defects and financial setbacks. Traditionally, the identification of microbial defects relies on the "probe and sniff technique" conducted approximately between the 10th and 12th month of aging. These potential defects, broadly classified into deep spoilage and surface defects, pose a significant hurdle for the ham industry.In this comprehensive study, we sampled and analyzed three defective dry-cured hams, exhibiting noticeable defects, and three normal hams carefully chosen from a producer in Andalusia, Spain. The objective was to scrutinize the microbiome of these samples to understand whether the observed defects were associated with shifts in the microbial population.16s multi-amplicon sequencing was performed using the Ion 16S Metagenomics Kit and Ion Torrent Sequencing Platform. Raw reads were then analysed using QIIME2 for data processing. Alpha-diversity and beta-diversity indexes, ANCOM test, Linear Discriminant Analysis (LEfSe) and co-occurrence network analysis were computed and visualized using the “microeco” R package.A pangenomic analysis and functional enrichment analysis of genomes available in the NCBI database was conducted.The analysis unveiled a distinctive association between Tetragenococcus, a genus recognized for its prevalence in fermented fish and vegetable products, as well as in cheese microbiota, and defective dry-cured hams. Both the LEfSe and ANCOM tests concurred in highlighting this taxon as a potential culprit.Subsequent scrutiny of Tetragenococcus genomes highlighted disparities between the two species T. koreensis and T. halophilus in terms of metabolic activity. Notably, T. koreensis manifested a distinctive set of genes encoding enzymes for carbohydrate metabolism. This study not only provided the opportunity to address the producer´s inquiry regarding the potential role of a specific microbial population in causing the defect, but also indicated the likelihood of a halotolerant microorganism being the culprit.While previous research has linked halotolerant microorganisms to defects in dry-cured meat, this represents the first time Tetragenococcus has been linked to such cases. This result sheds light on Tetragenococcus´ involvement in defected dry-cured hams.Ongoing investigations will focus on identifying the specific Tetragenococcus strains responsible for these defects, helping to refine our knowledge of their impact on dry-cured ham production.
publishDate 2024
dc.date.none.fl_str_mv 2024
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info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/257507
Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights; 28th International Conference on Food Microbiology and Hygiene; Burgos; España; 2024; 156-157
CONICET Digital
CONICET
url http://hdl.handle.net/11336/257507
identifier_str_mv Unveiling the culprit halotolerant tetragenococcus in multi-amplicon microbiome analysis of defective dry cured hams and pangenomic insights; 28th International Conference on Food Microbiology and Hygiene; Burgos; España; 2024; 156-157
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://foodmicro2024.com/ABSTRACT_FOOD_MICRO_2024_V2.pdf
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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/
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application/pdf
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dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv International Committee on Food Microbiology and Hygiene
publisher.none.fl_str_mv International Committee on Food Microbiology and Hygiene
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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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