Aquaculture facility-specific microbiota shape the zebrafish gut microbiome

Area of Science:

• Microbiology
• Aquaculture Science
• Host-Microbe Interactions

Background:

• Environmental microbiomes in recirculating aquaculture systems (RAS) impact host-associated microbial communities.
• Zebrafish (Danio rerio) research can experience confounding experimental outcomes due to uncontrolled variations in host-associated microbial communities across facilities.
• Limited studies have characterized both water and fish microbiomes across multiple independent facilities to assess environmental microbiome variation's impact on host microbiomes.

Purpose of the Study:

• To compare water and zebrafish gut microbiomes across five aquaculture facilities in the US and Norway.
• To evaluate the influence of environmental microbiome variation on host-associated microbial communities in zebrafish.
• To assess the consequences of environmental microbiome variation on the reproducibility of zebrafish microbiome studies.

Main Methods:

• Utilized a nested sampling design across five aquaculture facilities (two US, three Norway).
• Employed 16S rRNA gene sequencing for microbial community analysis of water and zebrafish gut samples.
• Applied Similarity Percentage analysis and Fast Expectation-Maximization for Microbial Source Tracking to identify microbial drivers and sources.

Main Results:

• Alpha diversity was higher in tank water than in fish guts; beta diversity clustered by sample type, facility, and location.
• Significant differences in microbial community composition were observed across facilities, with distinct facility-specific profiles in both water and fish.
• Tank water microbiota measurably contributed to zebrafish gut communities, with microbial similarity decreasing with geographic and facility distance.

Conclusions:

• Zebrafish aquaculture systems harbor unique microbial communities influenced by environmental and geographic factors.
• Tank water serves as a potential source for gut-associated microbes in zebrafish, impacting host microbiome composition.
• Incorporating environmental microbiome assessments is crucial for zebrafish experimental design to enhance reproducibility and interpretation in host-microbe interaction studies.