解析烏魚腸道的微生物群落和交互作用
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2021
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The animal gastrointestinal tract fosters a vast and complex population of microbes known as the gut microbiota, which plays crucial roles in host health and development. Microbial ecologists have used next generation sequencing (NGS) technologies to gather data on diverse microbial communities from all kinds of environmental samples. Consequently, much attention has focused on using bacterial symbiosis in the fish gut to elucidate host-microbe interactions, and its responses to environmental and host-specific factors. However, little is known about how fish gut microbiota respond when their fish hosts migrate or move across habitats. The grey mullet (Mugil cephalus L.) is an important fishery and aquaculture species in many countries. The species is a well-known catadromous species that migrates several times over its different life stages. For example, grey mullet eggs are laid in seawater environment, young fish first develop in the ocean and then migrate to brackish and freshwater to grow into adults before migrating back into ocean to reproduce during the breeding season. Interestingly, three grey mullet cryptic species migrate into the Taiwan strait from various migration routes to produce offspring. This fascinating life history–involving crossing between ecosystems makes the grey mullet an ideal model organism for studying the influence of migration and salinity transition on the structure of gut microbiota. Therefore, I conducted a comprehensive study in five chapters to investigate the influence of migration and changes in water regimes on the gut microbial community of the grey mullet. The first chapter includes background information and objectives of the study, and the second presents our findings on the diversity and composition of gut microbial communities in wild migrating fish into breeding grounds to clarify how host genetic background and historical environmental microflora influences on the the fish gut microbiota composition. We found that the bacteria in the gut communities of three cryptic species ofthe M. cephalus species complex are strongly influenced by host genetic variations, while long-distance migration governs the structure of the gut microbiota. Our results suggest that rapidly changes in salinity are an important factor shaping the fish gut microbial communities. For that reason, in Chapter 3, I mainly focus on how salinity change affects the structure and composition of gut microflora by examining an artificial transition from seawater to freshwater. Our results revealed that the transitioned fish had a different bacterial community compared to the fish maintained in seawater. Furthermore, microbial interaction networks were generated to deeply understand how microbial interactions change in response to environmental perturbation. Using the generalized Lotka-Volterra model, we generated two different complex interaction networks in the two treated groups, and found that many rare and low-abundant species were actually very important in the community because they formed a high number of connections to other microbial members. These results suggest that changes in salinity not only strong influence the complexity of the gut community, but also enhance the roles of keystone taxa in interaction networks. To validate the robustness of the interaction network model, Chapter 4 describes feeding trials using Enterococcus faecalis as a representative of the keystone taxa Enterococcaceae to validate the interactions inferred in the previous chapter. The changes in the relative abundance of Enterococcaceae and the bacterial families they interact with are investigated to clarify their relationships. Finally, in Chapter 5 thesis, I provide some general conclusions and discuss ways to improve our “observation-modelling-validation” framework to make it into a method for investigating gut microbiota dynamics that will be a tool to 1) predict the stability and reactivity of microbial populations in response to environmental disturbance and, 2) identify the key microbial interactions that have the potential to be widely applied in aquaculture.
The animal gastrointestinal tract fosters a vast and complex population of microbes known as the gut microbiota, which plays crucial roles in host health and development. Microbial ecologists have used next generation sequencing (NGS) technologies to gather data on diverse microbial communities from all kinds of environmental samples. Consequently, much attention has focused on using bacterial symbiosis in the fish gut to elucidate host-microbe interactions, and its responses to environmental and host-specific factors. However, little is known about how fish gut microbiota respond when their fish hosts migrate or move across habitats. The grey mullet (Mugil cephalus L.) is an important fishery and aquaculture species in many countries. The species is a well-known catadromous species that migrates several times over its different life stages. For example, grey mullet eggs are laid in seawater environment, young fish first develop in the ocean and then migrate to brackish and freshwater to grow into adults before migrating back into ocean to reproduce during the breeding season. Interestingly, three grey mullet cryptic species migrate into the Taiwan strait from various migration routes to produce offspring. This fascinating life history–involving crossing between ecosystems makes the grey mullet an ideal model organism for studying the influence of migration and salinity transition on the structure of gut microbiota. Therefore, I conducted a comprehensive study in five chapters to investigate the influence of migration and changes in water regimes on the gut microbial community of the grey mullet. The first chapter includes background information and objectives of the study, and the second presents our findings on the diversity and composition of gut microbial communities in wild migrating fish into breeding grounds to clarify how host genetic background and historical environmental microflora influences on the the fish gut microbiota composition. We found that the bacteria in the gut communities of three cryptic species ofthe M. cephalus species complex are strongly influenced by host genetic variations, while long-distance migration governs the structure of the gut microbiota. Our results suggest that rapidly changes in salinity are an important factor shaping the fish gut microbial communities. For that reason, in Chapter 3, I mainly focus on how salinity change affects the structure and composition of gut microflora by examining an artificial transition from seawater to freshwater. Our results revealed that the transitioned fish had a different bacterial community compared to the fish maintained in seawater. Furthermore, microbial interaction networks were generated to deeply understand how microbial interactions change in response to environmental perturbation. Using the generalized Lotka-Volterra model, we generated two different complex interaction networks in the two treated groups, and found that many rare and low-abundant species were actually very important in the community because they formed a high number of connections to other microbial members. These results suggest that changes in salinity not only strong influence the complexity of the gut community, but also enhance the roles of keystone taxa in interaction networks. To validate the robustness of the interaction network model, Chapter 4 describes feeding trials using Enterococcus faecalis as a representative of the keystone taxa Enterococcaceae to validate the interactions inferred in the previous chapter. The changes in the relative abundance of Enterococcaceae and the bacterial families they interact with are investigated to clarify their relationships. Finally, in Chapter 5 thesis, I provide some general conclusions and discuss ways to improve our “observation-modelling-validation” framework to make it into a method for investigating gut microbiota dynamics that will be a tool to 1) predict the stability and reactivity of microbial populations in response to environmental disturbance and, 2) identify the key microbial interactions that have the potential to be widely applied in aquaculture.
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微生物群落, 烏魚, 微生物交互, gut microbiome, fish microbiota, host-microbe interaction, microbial interaction, grey mullet, Mugil cephalus, validate interaction network