Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Stocking methods are used in the Province of Quebec to restore Salmo salar
populations. However, Atlantic salmon stocked juveniles show higher
mortality rates than wild ones when introduced into nature. Hatchery
environment, which greatly differs from the natural environment, is
identified as the main driver of the phenotypic mismatch between captive
and wild parrs. The latter is also suspected to impact the gut microbiota
composition, which can be associated with essential metabolic functions
for their host. We hypothesized that hatchery raised parrs potentially
recruit gut microbial communities that are different from those recruited
in the wild. This study evaluated the impacts of artificial rearing on gut
microbiota composition in 0+ parrs meant for stocking in two distinct
Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking
differences between hatchery and wild born parrs’ gut microbiota suggest
that microbiota could be another factor that could impact their survival
in the targeted river, since the microbiome is narrowly related to host
physiology. For instance, major commensals belonging to Enterobacteriaceae
and Clostridiacea from wild parrs’ gut microbiota were substituted in
captive parrs by lactic acid bacteria from the Lactobacillaceae family.
Overall, captive parrs host a generalist bacterial community whereas wild
parrs’ microbiota is much more specialized. This is the very first study
demonstrating extensive impact of captive rearing on intestinal microbiota
composition in Atlantic salmon intended for wild population stocking. Our
results strongly suggest the need to implement microbial ecology concepts
into conservation management of endangered salmon stocks supplemented with
hatchery reared parrs.