Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome
Abstract Background High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still...
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BMC
2025-06-01
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| Series: | Animal Microbiome |
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| Online Access: | https://doi.org/10.1186/s42523-025-00418-8 |
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| author | Judith Guitart-Matas Arturo Vera-Ponce de León Phillip B. Pope Torgeir R. Hvidsten Lorenzo Fraile Maria Ballester Yuliaxis Ramayo-Caldas Lourdes Migura-Garcia |
| author_facet | Judith Guitart-Matas Arturo Vera-Ponce de León Phillip B. Pope Torgeir R. Hvidsten Lorenzo Fraile Maria Ballester Yuliaxis Ramayo-Caldas Lourdes Migura-Garcia |
| author_sort | Judith Guitart-Matas |
| collection | DOAJ |
| description | Abstract Background High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment. Results The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis. Conclusions Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship. |
| format | Article |
| id | doaj-art-17104237f8eb4389b47cc25fd6cded0a |
| institution | OA Journals |
| issn | 2524-4671 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
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| series | Animal Microbiome |
| spelling | doaj-art-17104237f8eb4389b47cc25fd6cded0a2025-08-20T02:37:36ZengBMCAnimal Microbiome2524-46712025-06-017111610.1186/s42523-025-00418-8Multi-omics surveillance of antimicrobial resistance in the pig gut microbiomeJudith Guitart-Matas0Arturo Vera-Ponce de León1Phillip B. Pope2Torgeir R. Hvidsten3Lorenzo Fraile4Maria Ballester5Yuliaxis Ramayo-Caldas6Lourdes Migura-Garcia7Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB)Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesFaculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life SciencesDepartment of Animal Production, School of Agrifood and Forestry Science and Engineering (ETSEA), University of LleidaAnimal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA)Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA)Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Autonomous University of Barcelona (UAB)Abstract Background High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment. Results The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis. Conclusions Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.https://doi.org/10.1186/s42523-025-00418-8MetatranscriptomicsMetagenome-assembled genomesPost-weaningSwineAntimicrobial resistance |
| spellingShingle | Judith Guitart-Matas Arturo Vera-Ponce de León Phillip B. Pope Torgeir R. Hvidsten Lorenzo Fraile Maria Ballester Yuliaxis Ramayo-Caldas Lourdes Migura-Garcia Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome Animal Microbiome Metatranscriptomics Metagenome-assembled genomes Post-weaning Swine Antimicrobial resistance |
| title | Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome |
| title_full | Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome |
| title_fullStr | Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome |
| title_full_unstemmed | Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome |
| title_short | Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome |
| title_sort | multi omics surveillance of antimicrobial resistance in the pig gut microbiome |
| topic | Metatranscriptomics Metagenome-assembled genomes Post-weaning Swine Antimicrobial resistance |
| url | https://doi.org/10.1186/s42523-025-00418-8 |
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