The present study has addressed the issue of dietary alterations on gut microbiota in fish by investigating modulation of the allochthonous and autochthonous bacterial gut community of Atlantic salmon following feeding with pea protein concentrate, soy protein concentrate, extracted sunflower, poultry by-product and feather meal. The results revealed that total allochthonous and total autochthonous bacteria isolated from the distal intestine (DI) were affected by dietary modulations. Total autochthonous bacteria in proximal intestine remained unaffected. Corynebacteriaceae dominated the allochthonous bacteria and Lactobacillaceae dominated the autochthonous bacteria community in proximal and DI indicating that the most abundant groups are not shifted by alternative proteins. Some variations were observed between the bacterial communities as result of dietary manipulations. Alternative protein sources resulted in no severe signs of enteritis. Vacuolization of the liver was unaffected by diet. Furthermore, addition of plant materials significantly affected production of acetic acid. Weight of pyloric-, proximal- and DI was influenced by diet, especially feather meal. Growth performance was significantly affected by inclusion of feather meal to the diet. In conclusion the results showed that pea protein concentrate and poultry by-products are suitable protein replacements for Atlantic salmon and that soy protein concentrate is a potential candidate.