Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore
Shen, Xueyan, Yu, Xiong Da, Xie, Shangzhe, Hsu, Chia Da, Domingos, Jose A., and Gibson-Kueh, Susan (2026) Temporal microbiome dynamics and fish health-associated dysbiosis in freshwater aquarium systems: a case study from River Wonders Singapore. Frontiers In Microbiology, 17. 1739391.
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Abstract
Introduction: Aquarium systems are engineered yet biologically dynamic ecosystems where microbial communities underpin nutrient cycling, organic matter decomposition and water quality regulation. These processes directly affect aquatic animal health.
Methods: This study conducted a two-month time series analysis of waterborne microbiomes across six freshwater exhibits at River Wonders, Singapore, using 16S rRNA gene sequencing. Exhibits were categorized as “Healthy” (LM, MJ, EE) or “Stressed” (P, MJR, RG) based on fish health, and as indoor or semi-indoor/outdoor by system design.
Results and discussion: Temporal fluctuations in microbial composition and diversity were evident over time, with distinct profiles between indoor and semi-indoor/outdoor. Potential opportunistic or pathogenic genera, including Edwardsiella, Flavobacterium, Aeromonas, Pseudomonas and Mycobacterium, were consistently among the 30 most abundant taxa. The most severe dysbiosis occurred in exhibit P, characterized by a transient Pseudomonas bloom (51.4%), loss of nitrifiers (Nitrosomonas, Nitrospira) and concurrent fish health issues. MJR and RG harbored persistent polymicrobial risks, while “Healthy” exhibits maintained relatively more balanced microbial communities with lower pathogen loads. Routine husbandry interventions (e.g., partial water changes, substrate cleaning) coincided with improved microbial evenness and reductions in opportunistic taxa. These findings highlight diagnostic potential of microbiome profiling to detect early dysbiosis and support evidence-based husbandry in managed aquatic systems.
| Item ID: | 92484 |
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| Item Type: | Article (Research - C1) |
| ISSN: | 1664-302X |
| Keywords: | 16S rRNA sequencing, aquarium microbiome, fish health, maintenance practices, microbiome dysbiosis, opportunistic pathogens |
| Copyright Information: | © 2026 Shen, Yu, Xie, Hsu, Domingos and Gibson-Kueh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
| Funders: | Mandai Wildlife Group, Singapore |
| Date Deposited: | 13 Jul 2026 05:47 |
| FoR Codes: | 31 BIOLOGICAL SCIENCES > 3107 Microbiology > 310703 Microbial ecology @ 70% 30 AGRICULTURAL, VETERINARY AND FOOD SCIENCES > 3009 Veterinary sciences > 300903 Veterinary bacteriology @ 30% |
| SEO Codes: | 11 COMMERCIAL SERVICES AND TOURISM > 1101 Environmentally sustainable commercial services and tourism > 110199 Environmentally sustainable commercial services and tourism not elsewhere classified @ 20% 18 ENVIRONMENTAL MANAGEMENT > 1803 Fresh, ground and surface water systems and management > 180301 Assessment and management of freshwater ecosystems @ 80% |
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