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

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Title: Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status.
Authors: Tort-Miró, Carla1,2 (AUTHOR), Lorenzo-Rebenaque, Laura3 (AUTHOR), Montoro-Dasi, Laura4 (AUTHOR), Vega, Santiago4 (AUTHOR), Rodríguez, Juan Carlos5 (AUTHOR), Ventero, María-Paz5 (AUTHOR), Pérez-Gracia, Maria Teresa6 (AUTHOR), Guitart-Matas, Judith1,2 (AUTHOR), Giler-Baquerizo, Noemí1,2 (AUTHOR), Marco-Fuertes, Ana4 (AUTHOR), D'Auria, Giuseppe7 (AUTHOR), Marin, Clara4 (AUTHOR) clara.marin@uchceu.es, Migura-Garcia, Lourdes1,2 (AUTHOR) lourdes.migura@irta.cat
Source: BMC Veterinary Research. 4/4/2025, Vol. 21 Issue 1, p1-14. 14p.
Document Type: Article
Subjects: Animal communities, Animal culture, Gut microbiota, Life sciences, Animal science, Swine farms
Author-Supplied Keywords: Antimicrobial resistance
Biological Sciences Microbiology Agricultural and Veterinary Sciences Animal Production Veterinary Sciences
Illumina sequencing
Intestinal microbiome
Nanopore sequencing
Pigs
Post-weaning diarrhoea
Swine
Abstract: 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. [ABSTRACT FROM AUTHOR]
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Author Affiliations: 1https://ror.org/012zh9h13 Animal Health Program (CReSA), Collaborating Centre of the World Organization for Animal Health for Research and Control of Emerging and Re-emerging Pig Diseases in Europe, Institute of Agrifood Research and Technology (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Catalonia, Spain
2https://ror.org/011jtr847 Unitat mixta d'Investigació IRTA-UAB en Sanitat Animal. Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Catalonia, Spain
3https://ror.org/01460j859 Institute of Science and Animal Technology, Universitat Politècnica de Valencia, 46022, Valencia, Spain
4https://ror.org/01tnh0829 Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU Universities, Alfara del Patriarca, 46115, Valencia, Spain
5https://ror.org/01azzms13 Microbiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIAL, 03010, Alicante, Spain
6https://ror.org/01tnh0829 Área de Microbiología, Departamento de Farmacia, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Alfara del Patriarca, 46115, Valencia, Spain
7https://ror.org/0116vew40 Sequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, FISABIO, 46020, Valencia, Spain
Full Text Word Count: 8961
ISSN: 1746-6148
DOI: 10.1186/s12917-025-04693-0
Accession Number: 184301331
Database: Veterinary Source
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Abstract: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. [ABSTRACT FROM AUTHOR]
ISSN:17466148
DOI:10.1186/s12917-025-04693-0