Yolk sac fry of Atlantic salmon were reared under two microbial conditions: 1) Hatched under germfree conditions, and then colonized one week post hatching by using untreated water from the local lake Jonsvatnet (conventionalized CVZ), or 2) Hatched and reared under conventional conditions, i.e., the bacteria present during hatching were associated with the eggs as they were delivered from the hatchery (conventionally reared CVR). The fry were reared at 7 °C throughout the yolk sac stage in tissue culture flasks, and the water quality was maintained by exchanging 60% of the water volume with sterile synthetic freshwater medium three times a week. Samples for characterization of gut and skin microbiota were taken 6, 9, and 12 weeks post hatching (wph). The guts were dissected out and collected individually in cryotubes. For samples taken at 6 and 9 wph, the body without the intestinal tract was used as proxy for the skin (sampled individually), whereas for the samples taken at 12 wph, the skin was carefully dissected off and frozen individually in cryo tubes. Total DRNA was extracted and DNase treated, and cDNA was synthesized and used as templates in PCR. The v3+v4 region of the 16S rRNA gene was amplified and the final amplicon library was sequenced on a MiSeq run.