Use of 16S rRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon (Salmo salar) fed diets with cellulose or non-starch polysaccharides from soy

Duplicate groups of Atlantic salmon (Salmo salar L.), kept in seawater, were fed fish meal-based cold-pelleted diets. Diets with non-starch polysaccharides (NSP), either cellulose, purified soybean NSP or extruded purified soybean NSP at a dietary level of 100 g kg−1, were compared with a diet without supplemental NSP and a diet with soybean meal in a 28-day feeding trial. Isolation and characterizations were limited to culturable bacteria and population levels of aerobic and facultative aerobic heterotrophic autochthonous (adherent) and allochthonous (transient) bacteria present in the mid and distal intestines of Atlantic salmon fed the five different diets estimated using traditional bacteriological techniques. The presence of an autochthonous microbiota was demonstrated using transmission electron microscopy. No significant effects of diet composition were observed on total population levels of culturable bacteria present in the digestive tract, but the study showed that the composition of the gut microbiota (autochthonous or allochthonous) was sensitive to dietary changes. A total of 752 culturable isolates from the intestines were characterized by biochemical and physiological properties. Of these, 188 isolates were further characterized by partial sequencing the 16S rRNA genes. Among these, 146 isolates belonged to 31 phylotypes that were >94% identical to previously described species. However, 42 isolates showed similarity <94% to species available at the National Center of Biotechnology Information. Several of the phylotypes identified in the present study have not been reported previously in the gastrointestinal (GI) tract of fish, including the Gram-negative bacteria Gelidibacter salicanalis, Pseudoalteromonas elyakovii, Psychrobacter aquimaris, Psychrobacter cibarius, Psychrobacter fozii, Psychrobacter maritimus, Psychrobacter okhotskensis and Psychrobacter psychrophilus. Among the Gram-positive bacteria identified were Arthrobacter bergeri, Arthrobacter psychrolactophilus, Arthrobacter rhombi, Bacillus pumilus, Bacillus subtilis, Exiguobacterium spp., Microbacterium oxydans, Planococcus maritimus, Sporosarcina ginsengisoli and several bacteria that have been described as unculturable previously. In addition, we identified Carnobacterium inhibens, a lactic acid bacterium that is not frequently isolated from the GI tract of fish. Psychrobacter cibarius was the dominant bacterial species and was isolated from the digestive tract of all fish investigated.