Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status

[EN] Background: Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mort...

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Autores: Tort-Miro, Carla, Montoro-Dasí, Laura, Vega, Santiago, Rodríguez, Juan Carlos, Ventero, María Paz, Pérez-Gracia, Maria Teresa, Guitart-Matas, Judith, Giler-Baquerizo, Noemi, Marco-Fuertes, Ana, D'Auria, Giuseppe, Marin, Clara, Migura-Garcia, Lourdes, Lorenzo-Rebenaque, Laura|||0000-0002-4759-258X
Tipo de recurso: artículo
Fecha de publicación:2025
País:España
Institución:Universitat Politècnica de València (UPV)
Repositorio:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
Idioma:inglés
OAI Identifier:oai:riunet.upv.es:10251/230555
Acceso en línea:https://riunet.upv.es/handle/10251/230555
Access Level:acceso abierto
Palabra clave:Antimicrobial resistance
Post-weaning diarrhoea
Nanopore sequencing
Illumina sequencing
Pigs
Swine
Intestinal microbiome
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oai_identifier_str oai:riunet.upv.es:10251/230555
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
title Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
spellingShingle Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
Tort-Miro, Carla
Antimicrobial resistance
Post-weaning diarrhoea
Nanopore sequencing
Illumina sequencing
Pigs
Swine
Intestinal microbiome
title_short Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
title_full Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
title_fullStr Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
title_full_unstemmed Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
title_sort Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
dc.creator.none.fl_str_mv Tort-Miro, Carla
Montoro-Dasí, Laura
Vega, Santiago
Rodríguez, Juan Carlos
Ventero, María Paz
Pérez-Gracia, Maria Teresa
Guitart-Matas, Judith
Giler-Baquerizo, Noemi
Marco-Fuertes, Ana
D'Auria, Giuseppe
Marin, Clara
Migura-Garcia, Lourdes
Lorenzo-Rebenaque, Laura|||0000-0002-4759-258X
author Tort-Miro, Carla
author_facet Tort-Miro, Carla
Montoro-Dasí, Laura
Vega, Santiago
Rodríguez, Juan Carlos
Ventero, María Paz
Pérez-Gracia, Maria Teresa
Guitart-Matas, Judith
Giler-Baquerizo, Noemi
Marco-Fuertes, Ana
D'Auria, Giuseppe
Marin, Clara
Migura-Garcia, Lourdes
Lorenzo-Rebenaque, Laura|||0000-0002-4759-258X
author_role author
author2 Montoro-Dasí, Laura
Vega, Santiago
Rodríguez, Juan Carlos
Ventero, María Paz
Pérez-Gracia, Maria Teresa
Guitart-Matas, Judith
Giler-Baquerizo, Noemi
Marco-Fuertes, Ana
D'Auria, Giuseppe
Marin, Clara
Migura-Garcia, Lourdes
Lorenzo-Rebenaque, Laura|||0000-0002-4759-258X
author2_role author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Departamento de Ciencia Animal
Instituto Universitario de Ciencia y Tecnología Animal
Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural
Generalitat de Catalunya
Agencia Estatal de Investigación
Repositorio Institucional de la Universitat Politècnica de València Riunet
dc.subject.none.fl_str_mv Antimicrobial resistance
Post-weaning diarrhoea
Nanopore sequencing
Illumina sequencing
Pigs
Swine
Intestinal microbiome
topic Antimicrobial resistance
Post-weaning diarrhoea
Nanopore sequencing
Illumina sequencing
Pigs
Swine
Intestinal microbiome
description [EN] Background: Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore. Results: Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005. Conclusions: This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.
publishDate 2025
dc.date.none.fl_str_mv 2025
2025-04-04
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://riunet.upv.es/handle/10251/230555
url https://riunet.upv.es/handle/10251/230555
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-125641OB-C21 EL TRASPLANTE DE LA MICROBIOTA FECAL COMO ALTERNATIVA A LOS ANTIMICROBIANOS PARA LA PREVENCION DE ENFERMEDADES ENTERICAS CAUSADAS POR ESCHERICHIA COLI Y SALMONELLA EN PORCINO
Agencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-125641OB-C22 BACTERIOFAGOS COMO NUEVA HERRAMIENTA DE DESINFECCION DIRIGIDA Y COMPLEMENTARIA A LA LIMPIEZA Y DESINFECCION EN GRANJA
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Reconocimiento - No comercial - Sin obra derivada (by-nc-nd)
http://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Springer (Biomed Central Ltd.)
publisher.none.fl_str_mv Springer (Biomed Central Ltd.)
dc.source.none.fl_str_mv reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
instname:Universitat Politècnica de València (UPV)
instname_str Universitat Politècnica de València (UPV)
reponame_str RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
collection RiuNet. Repositorio Institucional de la Universitat Politécnica de Valéncia
repository.name.fl_str_mv
repository.mail.fl_str_mv
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spelling Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health statusTort-Miro, CarlaMontoro-Dasí, LauraVega, SantiagoRodríguez, Juan CarlosVentero, María PazPérez-Gracia, Maria TeresaGuitart-Matas, JudithGiler-Baquerizo, NoemiMarco-Fuertes, AnaD'Auria, GiuseppeMarin, ClaraMigura-Garcia, LourdesLorenzo-Rebenaque, Laura|||0000-0002-4759-258XAntimicrobial resistancePost-weaning diarrhoeaNanopore sequencingIllumina sequencingPigsSwineIntestinal microbiome[EN] Background: Antibiotics are used in animal husbandry to control infectious diseases. Different stressors can compromise animal health, leaving piglets vulnerable to pathogens, especially enterotoxigenic Escherichia coli (ETEC), which causes post-weaning diarrhoea (PWD), the major source of mortality and morbidity in swine production. Furthermore, PWD is a recurrent disease for certain farms, suggesting a link between gut microbial composition and animal health. The aim of this study was to identify the intestinal microbiota of pigs on farms with high health status (HHS) and low health status (LHS) to determine the relationships between sanitary status and gut health. Therefore, three pig farms with LHS presenting recurrent problems of PWD and three farms with HHS were selected to characterise the intestinal microbiome of sows and their piglets. 16 S rRNA gene sequencing technology was used to determine the associations of the gut microbiome with health. With the aim of bringing the MinION Nanopore device to the field for its portability and taxonomic resolution, the results obtained with Illumina were compared to those obtained with Nanopore. Results: Overall, the results indicated remarkable differences in intestinal microbial communities between animals from LHS farms and those from HHS farms, suggesting that the microbiomes of LHS animals were enriched with potential pathogenic microorganisms, mainly from the Pseudomonadota phylum, such as the genus Escherichia-Shigella, and their associated related species. Moreover, animals from HHS were enriched with beneficial microorganisms, such as Lactobacillus spp., Christensenellaceae R7 group, Treponema, Acetitomaculum and Oscillospiraceae UCG-005. Conclusions: This study identifies potential microorganisms that may contribute to health and disease in pig farms with HHS and LHS, suggesting that tracking their occurrence might provide insight into sanitary conditions. Moreover, this research highlights the compatibility between Illumina and Nanopore sequencing platforms, justifying the use of MinION Nanopore device in field applications for in situ studies of PWD. This application has the potential to enhance sustainable economic growth in swine farms by enabling more effective monitoring and management of animal health.This study was funded by the I+D+I National Program PID2021- 125641OB-C22 and PID2021-125641OB-C21. We also acknowledge the CERCA program (Generalitat de Catalunya). Carla Tort-Miró is a PhD student from the Autonomous University of Barcelona, Microbiology Program, with an IRTA fellowship.Springer (Biomed Central Ltd.)Departamento de Ciencia AnimalInstituto Universitario de Ciencia y Tecnología AnimalEscuela Técnica Superior de Ingeniería Agronómica y del Medio NaturalGeneralitat de CatalunyaAgencia Estatal de InvestigaciónRepositorio Institucional de la Universitat Politècnica de València Riunet20252025-04-04journal articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://riunet.upv.es/handle/10251/230555reponame:RiuNet. Repositorio Institucional de la Universitat Politécnica de Valénciainstname:Universitat Politècnica de València (UPV)InglésengAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-125641OB-C21 EL TRASPLANTE DE LA MICROBIOTA FECAL COMO ALTERNATIVA A LOS ANTIMICROBIANOS PARA LA PREVENCION DE ENFERMEDADES ENTERICAS CAUSADAS POR ESCHERICHIA COLI Y SALMONELLA EN PORCINOAgencia Estatal de Investigación http://dx.doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2021-2023 PID2021-125641OB-C22 BACTERIOFAGOS COMO NUEVA HERRAMIENTA DE DESINFECCION DIRIGIDA Y COMPLEMENTARIA A LA LIMPIEZA Y DESINFECCION EN GRANJAopen accesshttp://purl.org/coar/access_right/c_abf2Reconocimiento - No comercial - Sin obra derivada (by-nc-nd) http://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:riunet.upv.es:10251/2305552026-06-13T07:49:27Z
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