Related Experiment Video
Updated: May 9, 2026
05:38
Generation, Maintenance, and Identification of Germ-Free Zebrafish Models from Larvae to Juvenile Stages
Published on: April 12, 2024
Aquaculture facility-specific microbiota shape the zebrafish gut microbiome
Kayla C Evens1,2, Ingrid Bakke3, Brendan J M Bohannan4
1Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA. kayla.c.evens@usn.no.
Animal Microbiome
|May 7, 2026
Summary
Zebrafish aquaculture facilities have unique microbial communities influenced by environment and geography. Tank water impacts fish gut microbes, but other factors like diet are primary drivers, affecting research reproducibility.
Area of Science:
- Microbiology
- Aquaculture Science
- Zebrafish Research
Background:
- Environmental microbiomes in recirculating aquaculture systems (RAS) influence host-associated microbial communities.
- Uncontrolled variation in zebrafish (Danio rerio) microbiomes across facilities can confound research outcomes.
- Limited characterization exists for tank water and fish microbiomes across multiple facilities.
Purpose of the Study:
- To compare water and zebrafish gut microbiomes across multiple independent aquaculture facilities.
- To evaluate the impact of environmental microbiome variation on host-associated microbial communities.
- To identify factors contributing to microbiome variation in zebrafish research.
Main Methods:
- 16S rRNA gene sequencing was used to analyze microbiomes.
- A nested sampling design across five aquaculture facilities (US and Norway) was employed.
- Microbial source tracking (FEAST) was utilized to assess water's contribution to gut microbiomes.
Main Results:
- Significant clustering of microbiomes by sample type, facility, and geography was observed.
- Facility identity explained the largest proportion of compositional variance in microbiomes.
- Key taxa like Cetobacterium, Vibrio, Aeromonas (fish gut) and Pseudomonas, Rheinheimera (water) drove facility differences.
Conclusions:
- Zebrafish facilities harbor distinct microbial communities shaped by environmental and geographic factors.
- While tank water influences gut microbiomes, unknown sources (diet, host physiology) are primary drivers of variation.
- Standardized reporting of environmental conditions and microbial composition is crucial for zebrafish research reproducibility.
