Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT)
Introduction: Tilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the indus...
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2025
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| Online Access: | https://hdl.handle.net/10568/177764 |
| _version_ | 1855530414641250304 |
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| author | Delamare-Deboutteville, Jerome Mahmuddin, Mahirah Han Ming, Gan Rodde, Charles Khor, Laura Verner-Jeffreys, David Chadag, Vishnumurthy Mohan Benzie, John |
| author_browse | Benzie, John Chadag, Vishnumurthy Mohan Delamare-Deboutteville, Jerome Han Ming, Gan Khor, Laura Mahmuddin, Mahirah Rodde, Charles Verner-Jeffreys, David |
| author_facet | Delamare-Deboutteville, Jerome Mahmuddin, Mahirah Han Ming, Gan Rodde, Charles Khor, Laura Verner-Jeffreys, David Chadag, Vishnumurthy Mohan Benzie, John |
| author_sort | Delamare-Deboutteville, Jerome |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Introduction: Tilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry’s reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential for identifying the characteristics that constitute a healthy microbial community.
Methods: In this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia. We compared them to those reared in earthen ponds on another farm in Malaysia.
Results: A total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species. Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%). At the same time, other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples exhibited notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition.
Discussion: These results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of practical microbiome monitoring strategies, such as early-warning tools for farm health, and inform targeted interventions to improve aquaculture performance. |
| format | Journal Article |
| id | CGSpace177764 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1777642025-12-13T02:10:10Z Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) Delamare-Deboutteville, Jerome Mahmuddin, Mahirah Han Ming, Gan Rodde, Charles Khor, Laura Verner-Jeffreys, David Chadag, Vishnumurthy Mohan Benzie, John fish genetically improved farmed tilapia (gift) microbiome analysis 16s v4 rrna sequencing amplicon sequence variants (asvs) principal coordinates analysis (pcoa) aquaculture systems (tank vs. pond) linear discriminant analyses (lda lefse) Introduction: Tilapia (Oreochromis spp.) are among the most widely cultivated freshwater finfish species worldwide. The industry increasingly relies on tilapia strains selected for improved growth and other traits, particularly the Genetically Improved Farmed Tilapia (GIFT) strain. Despite the industry’s reliance on tilapia, knowledge of microbiome dynamics in reared tilapia remains limited. Understanding normal successional patterns in the microbiome of farmed tilapia is essential for identifying the characteristics that constitute a healthy microbial community. Methods: In this study, we assessed the microbiomes of tank and pond-reared GIFT tilapia by analyzing 568 samples, including water, gut, skin, and gill microbiomes of tilapia, from tank systems housing the source GIFT populations in Malaysia. We compared them to those reared in earthen ponds on another farm in Malaysia. Results: A total of 2,307 amplicon sequence variants (ASVs) were identified, encompassing a broad taxonomic diversity of 39 phyla, 86 classes, 180 orders, 299 families, 501 genera, and 399 species. Our findings elucidated distinct microbial community structures between rearing environments and across fish tissues, shedding light on intricate host-microbe interactions shaped by environmental conditions and management practices. The gut microbiome of tank-reared tilapia was dominated by Fusobacteriota (71.14%), in contrast to pond-reared fish (22%). At the same time, other taxa, such as Bacteroidota, Firmicutes_A, and Cyanobacteria, also varied markedly between environments and sampling periods. Skin and gill samples exhibited notable variability in the relative abundances of Fusobacteriota and Deinococcota between the two rearing sites. Principal Coordinates Analysis (PCoA) highlighted the distinct clustering of samples by rearing environment, particularly within gut microbiomes. Biomarkers such as Cyanobiaceae (pond water) and Sphingomonadaceae (tank water) underscored the impact of rearing conditions on microbial composition. Discussion: These results establish valuable baseline information on the types of bacteria associated with healthy, genetically defined (GIFT) tilapia strains. This foundational information will help identify specific microbial taxa associated with beneficial or detrimental effects on tilapia health and productivity across varying rearing conditions. Such insights can guide the development of practical microbiome monitoring strategies, such as early-warning tools for farm health, and inform targeted interventions to improve aquaculture performance. 2025-11-11T05:38:19Z 2025-11-11T05:38:19Z Journal Article https://hdl.handle.net/10568/177764 en Open Access application/pdf Frontiers Media Jerome Delamare-Deboutteville, Mahirah Mahmuddin, Gan Han Ming, Charles Rodde, Laura Khor, David Verner-Jeffreys, Vishnumurthy Mohan Chadag, John Benzie. (1/9/2025). Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT). Frontiers in Microbiomes, 4. |
| spellingShingle | fish genetically improved farmed tilapia (gift) microbiome analysis 16s v4 rrna sequencing amplicon sequence variants (asvs) principal coordinates analysis (pcoa) aquaculture systems (tank vs. pond) linear discriminant analyses (lda lefse) Delamare-Deboutteville, Jerome Mahmuddin, Mahirah Han Ming, Gan Rodde, Charles Khor, Laura Verner-Jeffreys, David Chadag, Vishnumurthy Mohan Benzie, John Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title | Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title_full | Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title_fullStr | Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title_full_unstemmed | Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title_short | Microbiome dynamics in tank- and pond-reared Genetically Improved Farmed Tilapia (GIFT) |
| title_sort | microbiome dynamics in tank and pond reared genetically improved farmed tilapia gift |
| topic | fish genetically improved farmed tilapia (gift) microbiome analysis 16s v4 rrna sequencing amplicon sequence variants (asvs) principal coordinates analysis (pcoa) aquaculture systems (tank vs. pond) linear discriminant analyses (lda lefse) |
| url | https://hdl.handle.net/10568/177764 |
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