The animal microbiota is closely linked to host health, contributing to metabolic processes, immune regulation, and defense against pathogens. The nasal microbiota has received relatively little attention compared with the gastrointestinal tract, despite its relevant role in respiratory health. Thus, investigating the nasal microbiota represents a promising strategy for improving the prevention and management of respiratory diseases. This thesis explores the establishment of the nasal microbiota in pigs, its detailed composition, and its association with the host immune system.
The first objective of this thesis was to improve the analysis of the nasal microbiota of piglets, resulting in an optimized pipeline, using DNA from nasal swabs and massive sequencing of a 16S rRNA gene fragment. Subsequently, it undergoes various processing steps to assign the taxonomy, calculate the relative abundance of each taxon, and perform different diversity and compositional analyses.
Next, to study the impact of sow-piglet contact in early life, the nasal microbiota of piglets in controlled environmental conditions but with varying durations of contact with their sows, was compared at weaning. Contact with sows proved to be a major factor affecting the nasal microbial composition of their offspring. Piglets with normal contact until weaning developed a nasal microbiota similar to that of healthy farm piglets, while limited or no contact led to altered microbiotas dominated by atypical taxa.
Besides, efforts to characterize the nasal microbiota composition of domestic pigs frequently report the presence of anaerobic bacteria typically found in the gut, such as Bacteroidales and Clostridiales, although their presence in the nasal cavity remains poorly understood. The findings in this thesis, not only confirmed the fecal origin of these bacteria, but also demonstrated that their detection in the nasal cavity is not artefactual. Furthermore, 16S rRNA cDNA analyses revealed that these taxa are metabolically active.
Among the microbes found in the microbiota, those with the potential of causing disease, called pathobionts, are of special interest. Here, the genomes of Mycoplasma hyorhinis strains coming from different clinical backgrounds were compared to identify virulence determinants. Despite most of the genes were shared across strains, we identified a cluster of health-associated strains with possible differential markers.
Finally, in the current scenario of antimicrobial use reduction in animal production, vaccination is critical. Nevertheless, individual variation in antibody response remains poorly understood. While the microbiota has been linked to antibody response, this has not yet been explored in the nasal microbiota of pigs. In this study, piglets with stronger antibody responses had more diverse nasal and rectal microbiotas. Moreover, swine core nasal colonizers, including Bacteroidales, Clostridiales, Moraxella, Staphylococcus and Neisseria were linked to higher antibody levels. In the gut, Clostridiales showed a positive and Enterobacteriales a negative association.
Globally, this thesis provides new insights into the development, composition, and immunological relevance of the nasal microbiota in pigs, paving the way for future strategies to promote respiratory health.
| Date of Award | 17 Oct 2025 |
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| Original language | English |
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| Awarding Institution | - Universitat Autònoma de Barcelona (UAB)
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| Supervisor | Virginia Aragón Fernández (Director) & Ana Maria Florencia Correa Fiz (Director) |
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