<p>Supporting information</p><p>Table S1: Sequence of freshwater bathing and faecal scoring events. Sampling order denotes the order in which cohorts were handled during each faecal measure event. Eve Date nt Comments Cohort Faecal Score (%) Pop. 1 3 3.5 4 5 Mar ine Inpu 4 Aug 2010 t 10x10m pen, Spirit Feed 2359 AG D Bat 22 Sep 2010 h 1 Bathed 2236 AG D Bat 21 Oct 10 h 2 Split and bathed to two 5x5m pens 2215 2-3 Nov 2010 Fae Starved pre-sample; split to four 5x5m pens cal Mea 0 sure . 1 IntPro 553 63.9 5.6 0 5 1.1 0 . LFM 553 74.6 5.6 0 5 1.3 1 . HiPro 550 51.1 8.9 0 8 3.5 1 . LoPro 557 48.9 11.9 0 3 4.2</p><p>1 AG D Bat 1-2 Dec 2010 h 3 Bathed 14-15 Dec 2010 Fae Starved from evening pre-sample cal Mea sure 2 2 IntPro 526 13.1 12 8.2 0 31.6 2 9 . LFM 532 5.6 2.6 25.4 3 18.6 1 8 . HiPro 528 16.9 6.1 19.4 2 13.7 3 7 . LoPro 524 5.3 3.2 14.9 8 32.1 AG D Bat 12-13Jan 2011 h 4 Bathed 25-27 Jan 2011 Fae Fed until sample cal Mea 8 sure . 3 IntPro 453 39.7 7.5 4.6 8 15 1 5 . LFM 470 22.6 21.7 3.2 1 13.4 HiPro 465 23.7 12.9 7.7 1 14.8 3 .</p><p>2 8 1 4 . LoPro 485 24.7 12.3 12.8 2 6.8 AG D Bat 23-25Feb 2011 h 5 Bathed 4-7 Mar 2011 Fae Fed until sample cal 1 Mea 6 sure . 4 IntPro 424 17.1 28.6 7 4 9.2 1 8 . LFM 420 18.8 16.9 10 8 12.9 2 8 . HiPro 405 13.6 11.4 9.4 7 17.3 2 2 . LoPro 426 14.8 23.8 12.8 1 8.6 4-6 Apr 2011 Fae Fed until sample cal 2 Mea 6 sure . 5 IntPro 384 20.2 17.8 9.4 2 2.4 3 2 . LFM 388 17.3 14.4 12.9 7 8.8 HiPro 379 19.5 13.2 12.1 2 8.2 5</p><p>3 . 3 1 4 . LoPro 416 26 14.2 18.8 2 4.8</p><p>4 Table S2: Multivariate Statistical comparison between Atlantic salmon GI tract microbial communities on the basis of sampling time, diet and categorised faecal properties.</p><p>P Unique P (Perma- permu- (Monte Factor df MS F nova) tations Carlo) Time 3 14432 6.0811 0.0001 9872 0.0001 Diet 3 13051 5.4991 0.0001 9891 0.0001 Faecal Score 4 8464.2 3.5665 0.0001 9866 0.0001 Time × Diet 9 3910.6 1.6478 0.0008 9799 0.001 Time × Faecal Score 12 2968.1 1.2506 0.0459 9783 0.0485 Diet × Faecal Score 12 2422.6 1.0208 0.4058 9805 0.4107 Time × Diet × Faecal Score 36 2661.6 1.1215 0.0798 9666 0.0924 Residuals 133 2373.3 Total 216</p><p>5 Table S3: Analysis of similarities comparison between categorised faecal properties. </p><p>Faecal Groups R Significance level (%) 2, 1 -0.009 71.4 2, 3 -0.007 60.4 2, 4 0.113 0.03 2, 3.5 0.094 0.20 1, 3 0.002 34.3 1, 4 0.185 0.01 1, 3.5 0.172 0.03 3, 4 0.101 0.10 3, 3.5 0.145 0.02 4, 3.5 0.038 3.00</p><p>6 Figure S1: Salmon growth and water temperature during the feeding trial. Average weight at each measure (Measure1 in November 2010 to Measure5 in April 2011), showing immature </p><p>(circles) and maturing (triangles) sub-populations within each ‘Cohort’; IntPro (Green), LFM </p><p>(Yellow), HiPro (Red), and LoPro (blue). Values are expressed as means ± SE. Temperatures are daily 5 metre readings. Long term average (LTA) temperatures for Meads Creek (Dover, </p><p>Tasmania) are shown for comparison.</p><p>7 Figure S2: Faecal score progression during the feeding trial. Showing immature (circles) and maturing (triangles) sub-populations within each ‘Cohort’; IntPro (Green), LFM (Yellow), </p><p>HiPro (Red), and LoPro (blue). Values are expressed as means ± SE.</p><p>8 Figure S3: Bacterial diversity at the class level as defined by a) sampling time and diet cohort; and b) faecal score factors. Faecal scores that are low (1 to 3) and high (3.5 and 4) are shown for comparison since communities were statistically distinguishable. a)</p><p> b)</p><p>9</p>