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Additional file 8: Figure S2. Specificity of the primers that target Lactobacillus and Mycoplasma genus. The results in figure summarise bacterial genus targeted by Lactobacillus (Fig. 1 A, B, C) and Mycoplasma (Fig. 1 D, E, F) specific primer set. It shows that of all genus captured by Lactobacillus primer pair 98% were Lactobacillus in fish 1, 78% in fish 2, and 65% in fish 3. While of all genus captured by Mycoplasma primer pair 95% were Mycoplasma in fish 1, 79% in fish 2, and 56% in fish 3.

Additional file 14: Figure S8. In vivo phenotypic fish performance fed on two different feeds. Figure visually represents different phenotypic performance data of fish (n=32 per feed) fed on two different feed. A Atlantic salmon length in centimetres; B Atlantic salmon length in weight in kilograms; C Atlantic salmon percentage carcass yield; D Atlantic salmon gonad weight in grams; E Atlantic salmon gutted weight in kilograms; F Atlantic salmon liver weight in grams. Blue box plots represent data from salmon (n=32) fed on Fish meal free diet, and red represents Atlantic salmon fed on Fish meal diet (n=32).

Additional file 1. Supplementary methods.

Additional file 7: Figure S1. Physiochemical conditions measured within different real Atlantic salmon gut compartments. 1A-1C measured physicochemical conditions within real salmon (n=3) gut compartments: pH (1A), temperature (°C, 1B), dissolved oxygen (mg/L, 1C).