Location: Cool and Cold Water Aquaculture Research
Project Number: 8082-10600-003-005-A
Project Type: Cooperative Agreement
Start Date: Aug 1, 2025
End Date: Jul 31, 2026
Objective:
Characterize the microbiome in trout during early developmental time periods in aquaculture and laboratory settings. Sub-objective 4.A. Compare the influence of farm vs laboratory environment on gut bacterial microbiota during a field trial using defined genetic lines of rainbow trout. Sub-objective 4.B. Identify key Archaea and eukaryote microbiota members that are different in juvenile and adult resistant and susceptible trout. Sub-objective 4.C Isolate commensal bacteria that are more abundant in resistant fish and characterize their interactions in vitro with defined pathogens to determine if this is a mechanism of resistance
Approach:
We are characterizing the microbiome of trout in early stages of development in laboratory and aquaculture settings. For subobjective 4a and b, we will isolate DNA from various tissues from trout raised in both settings and using next generation sequencing to identify bacteria, archaea, and fungal species in the samples. DNA will be extracted using commercial DNA isolation kits. The 16S rRNA gene will be sequenced to determine the composition of the microbiome in various trout tissues. We will also characterize the archaea and fungal species in the samples using primers specific for those phyla. This analysis will be performed on lines of trout that are resistant or sensitive to common trout pathogens, Flavobacterium columnare and F. psychrophilum.
For sub-objective 4c, we will isolate microbes that we identify as having the potential to confer resistance to pathogens. This may be due to increased abundance in 4a or 4b, but may also be based on research. We will use in vitro assays to determine how the trout microbiota members interact with each other on various types of media and in the presence of more complex communities. We will use assays such as quantification of biofilm formation using crystal violet staining and quantification, imaging for physical contact and biofilm dynamics, differential centrifugation to separate components of the microbe to determine if they affect the interactions, and fluorescent tagging to determine how the microbes effect other microbes that are associated with trout.