Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings
ABSTRACT The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon,...
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American Society for Microbiology
2025-05-01
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| Series: | Microbiology Spectrum |
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| Online Access: | https://journals.asm.org/doi/10.1128/spectrum.01989-24 |
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| author | Melissa Soh Shuan Er Adrian Low Zeehan Jaafar Richard de Boucher Henning Seedorf |
| author_facet | Melissa Soh Shuan Er Adrian Low Zeehan Jaafar Richard de Boucher Henning Seedorf |
| author_sort | Melissa Soh |
| collection | DOAJ |
| description | ABSTRACT The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.IMPORTANCEUnderstanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices. |
| format | Article |
| id | doaj-art-afeab9c8946f45bcbb1e2de37be94f88 |
| institution | DOAJ |
| issn | 2165-0497 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | American Society for Microbiology |
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| series | Microbiology Spectrum |
| spelling | doaj-art-afeab9c8946f45bcbb1e2de37be94f882025-08-20T03:11:32ZengAmerican Society for MicrobiologyMicrobiology Spectrum2165-04972025-05-0113510.1128/spectrum.01989-24Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settingsMelissa Soh0Shuan Er1Adrian Low2Zeehan Jaafar3Richard de Boucher4Henning Seedorf5Temasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences Laboratory, Singapore, SingaporeDepartment of Biological Sciences, National University of Singapore, Singapore, SingaporeTemasek Life Sciences Laboratory, Singapore, SingaporeTemasek Life Sciences Laboratory, Singapore, SingaporeABSTRACT The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.IMPORTANCEUnderstanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.https://journals.asm.org/doi/10.1128/spectrum.01989-24fish gut microbiotaaquacultureAsian seabassfish microbiomemicrobial ecologyfish pathogens |
| spellingShingle | Melissa Soh Shuan Er Adrian Low Zeehan Jaafar Richard de Boucher Henning Seedorf Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings Microbiology Spectrum fish gut microbiota aquaculture Asian seabass fish microbiome microbial ecology fish pathogens |
| title | Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings |
| title_full | Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings |
| title_fullStr | Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings |
| title_full_unstemmed | Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings |
| title_short | Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings |
| title_sort | spatial and temporal changes in gut microbiota composition of farmed asian seabass lates calcarifer in different aquaculture settings |
| topic | fish gut microbiota aquaculture Asian seabass fish microbiome microbial ecology fish pathogens |
| url | https://journals.asm.org/doi/10.1128/spectrum.01989-24 |
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