Inter-individual variation in the dominant intestinal microbiota of reared Atlantic cod (Gadus morhua L.) larvae

The diversity of the microbiota in 15 Atlantic cod (Gadus morhua L.) larvae from three different hatcheries with variable food type and water treatment was characterized with culture dependent and independent approaches. The culture-dependent approach was phenotypic characterization of bacterial isolates based on 16 tests, and the culture-independent approach was terminal restriction fragment length polymorphism (T-RFLP) of PCR amplified 16S rRNA. Both approaches revealed large inter-individual differences in the microbiota of cod larvae. Data from real time PCR indicate substantially lower variation in bacterial number larva-1 both within and between hatcheries than the data on colony forming units, resulting in an estimated four orders of magnitude variation in culturability between larvae. Considerably higher richness and diversity were observed with T-RFLP than with phenotypic characterization, and no correlation between the two approaches was found for diversity indexes calculated at the individual level. Dissimilarity in the composition of the microbiota between individuals from the same rearing environment was comparable to the dissimilarities between hatcheries. The large inter-individual variation is important to consider when designing experiments, as pooling of individuals will completely mask this variability. We conclude that colonization of individual cod larvae by bacteria seems to be a stochastic and not a deterministic process, which is not well understood.