Publicação
Prevalence and genetic characterization of pathogenic mycobacteria in fish
| Resumo: | The microbiome of marine fish, especially those along the Portuguese coast, has been largely overlooked. However, bacterial infections pose significant risks to animal health, human safety, the fish industry, and the broader environment. To address this knowledge gap, this MSc thesis investigated the microbial communities associated with natural populations of two commercially important fish species: Merluccius merluccius (hake) and Trisopterus luscus (pout). The specific objectives included assessing how various factors - particularly fish species, tissue type, fishing location, and season - influence the general microbiome composition. Following sample collection, multiple DNA extraction methods were tested and optimized to identify the most effective protocols for each tissue type. DNA metabarcoding was conducted using the 16S rRNA gene to characterize microbiome composition and diversity, with data analysis performed through various bioinformatics tools. The majority of the identified OTUs belonged to the phylum Proteobacteria, indicating its significant role in fish bacterial communities; this trend was consistent across all samples. Trisopterus luscus exhibited greater variability in OTUs, suggesting it harbours substantial microbial diversity, particularly during the summer, whereas Merluccius merluccius showed consistent results, dominated almost exclusively by Proteobacteria. Within the phylum Actinobacteria, the order Corynebacteriales (which includes Mycobacterium) was the most prevalent. T. luscus showed marked seasonal shifts, with warmer temperatures favouring Corynebacteriales, with most of the Mycobacterium identifications with hits corresponding to M. simiae, and cooler temperatures favouring Micrococcales. For M. merluccius, location had a notable impact on microbial diversity, particularly in winter and spring. All analysed factors, as well as their interactions, had a significant effect on the structure of the general bacterial community. For Actinobacteria, fish species and season showed a significant effect, while tissue type played a less influential role. This study underscores the utility of 16S rRNA gene analysis, combined with DNA metabarcoding, as a valuable approach for characterizing bacterial microbiomes in marine fish. The findings provide new insights into marine microbiomes, their responses to environmental factors, and their implications for fish health and ecosystem stability. |
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| Autores principais: | Tomé, Mónica Isabel Garcia |
| Assunto: | Bacterial community Fish microbiome Mycobacteria Zoonose Comunidade bacteriana Microbioma dos peixes Micobactérias |
| Ano: | 2024 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso aberto |
| Instituição associada: | Universidade do Minho |
| Idioma: | inglês |
| Origem: | RepositóriUM - Universidade do Minho |
| Resumo: | The microbiome of marine fish, especially those along the Portuguese coast, has been largely overlooked. However, bacterial infections pose significant risks to animal health, human safety, the fish industry, and the broader environment. To address this knowledge gap, this MSc thesis investigated the microbial communities associated with natural populations of two commercially important fish species: Merluccius merluccius (hake) and Trisopterus luscus (pout). The specific objectives included assessing how various factors - particularly fish species, tissue type, fishing location, and season - influence the general microbiome composition. Following sample collection, multiple DNA extraction methods were tested and optimized to identify the most effective protocols for each tissue type. DNA metabarcoding was conducted using the 16S rRNA gene to characterize microbiome composition and diversity, with data analysis performed through various bioinformatics tools. The majority of the identified OTUs belonged to the phylum Proteobacteria, indicating its significant role in fish bacterial communities; this trend was consistent across all samples. Trisopterus luscus exhibited greater variability in OTUs, suggesting it harbours substantial microbial diversity, particularly during the summer, whereas Merluccius merluccius showed consistent results, dominated almost exclusively by Proteobacteria. Within the phylum Actinobacteria, the order Corynebacteriales (which includes Mycobacterium) was the most prevalent. T. luscus showed marked seasonal shifts, with warmer temperatures favouring Corynebacteriales, with most of the Mycobacterium identifications with hits corresponding to M. simiae, and cooler temperatures favouring Micrococcales. For M. merluccius, location had a notable impact on microbial diversity, particularly in winter and spring. All analysed factors, as well as their interactions, had a significant effect on the structure of the general bacterial community. For Actinobacteria, fish species and season showed a significant effect, while tissue type played a less influential role. This study underscores the utility of 16S rRNA gene analysis, combined with DNA metabarcoding, as a valuable approach for characterizing bacterial microbiomes in marine fish. The findings provide new insights into marine microbiomes, their responses to environmental factors, and their implications for fish health and ecosystem stability. |
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