Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status
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 m...
Saved in:
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-04-01
|
| Series: | BMC Veterinary Research |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12917-025-04693-0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849734848020742144 |
|---|---|
| author | Carla Tort-Miró Laura Lorenzo-Rebenaque Laura Montoro-Dasi Santiago Vega Juan Carlos Rodríguez María-Paz Ventero Maria Teresa Pérez-Gracia Judith Guitart-Matas Noemí Giler-Baquerizo Ana Marco-Fuertes Giuseppe D’Auria Clara Marin Lourdes Migura-Garcia |
| author_facet | Carla Tort-Miró Laura Lorenzo-Rebenaque Laura Montoro-Dasi Santiago Vega Juan Carlos Rodríguez María-Paz Ventero Maria Teresa Pérez-Gracia Judith Guitart-Matas Noemí Giler-Baquerizo Ana Marco-Fuertes Giuseppe D’Auria Clara Marin Lourdes Migura-Garcia |
| author_sort | Carla Tort-Miró |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-fabfb0f10713422d84d593101efe6ea9 |
| institution | DOAJ |
| issn | 1746-6148 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Veterinary Research |
| spelling | doaj-art-fabfb0f10713422d84d593101efe6ea92025-08-20T03:07:41ZengBMCBMC Veterinary Research1746-61482025-04-0121111410.1186/s12917-025-04693-0Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health statusCarla Tort-Miró0Laura Lorenzo-Rebenaque1Laura Montoro-Dasi2Santiago Vega3Juan Carlos Rodríguez4María-Paz Ventero5Maria Teresa Pérez-Gracia6Judith Guitart-Matas7Noemí Giler-Baquerizo8Ana Marco-Fuertes9Giuseppe D’Auria10Clara Marin11Lourdes Migura-Garcia12Animal 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)Institute of Science and Animal Technology, Universitat Politècnica de ValenciaFacultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU UniversitiesFacultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU UniversitiesMicrobiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIALMicrobiology Department, Dr. Balmis University General Hospital, Microbiology Division, Miguel Hernández University, ISABIALÁrea de Microbiología, Departamento de Farmacia, Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU UniversitiesAnimal 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)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)Facultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU UniversitiesSequencing and Bioinformatics Service, Foundation for the Promotion of Health and Biomedical Research of Valencia Region, FISABIOFacultad de Veterinaria, Instituto de Ciencias Biomédicas, Universidad Cardenal Herrera-CEU, CEU UniversitiesAnimal 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)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.https://doi.org/10.1186/s12917-025-04693-0Antimicrobial resistancePost-weaning diarrhoeaNanopore sequencingIllumina sequencingPigsSwine |
| spellingShingle | Carla Tort-Miró Laura Lorenzo-Rebenaque Laura Montoro-Dasi Santiago Vega Juan Carlos Rodríguez María-Paz Ventero Maria Teresa Pérez-Gracia Judith Guitart-Matas Noemí Giler-Baquerizo Ana Marco-Fuertes Giuseppe D’Auria Clara Marin Lourdes Migura-Garcia Nanopore versus Illumina to study the gut bacterial diversity of sows and piglets between farms with high and low health status BMC Veterinary Research Antimicrobial resistance Post-weaning diarrhoea Nanopore sequencing Illumina sequencing Pigs Swine |
| title | 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_short | 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 |
| topic | Antimicrobial resistance Post-weaning diarrhoea Nanopore sequencing Illumina sequencing Pigs Swine |
| url | https://doi.org/10.1186/s12917-025-04693-0 |
| work_keys_str_mv | AT carlatortmiro nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT lauralorenzorebenaque nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT lauramontorodasi nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT santiagovega nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT juancarlosrodriguez nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT mariapazventero nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT mariateresaperezgracia nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT judithguitartmatas nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT noemigilerbaquerizo nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT anamarcofuertes nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT giuseppedauria nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT claramarin nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus AT lourdesmiguragarcia nanoporeversusilluminatostudythegutbacterialdiversityofsowsandpigletsbetweenfarmswithhighandlowhealthstatus |