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Figure S1 Proportional contribution of chloroplast 16S rRNA gene sequences (derived mainly from dietary lupin meal kernel) in all salmon faecal samples across the survey period for each diet group, demonstrating community shifts and overall salmon specimen variability. Data derived from bacterial 16S rRNA pyrosequencing analysis.

Figure S2 Relative major abundance of bacterial species in the gastrointestinal tract of Atlantic salmon from five different seasons: (a) first winter; (b) spring; (c) summer; (d) autumn; and (e) second winter.

Table S1 AGD treatment and freshwater bathing schedule and time of sampling.

Table S2 Comparison of microbial community structure with response to (a) diet and season and (b) diet and month using permanova.

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