Additional file 7 of SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic salmon GI tract and associated microbial communities

Additional file 6: Table S5. Bacterial group responses to feed change within different gut compartments in real salmon and SalmoSim based on qPCR data. The table summarises the Estimated Marginal Means output for each mixed-effect linear model run with different qPCR measured relative abundance values identifying the difference between real salmon and SalmoSim response to feed change (Fish meal to Fish meal free diet) within different gut compartments (S – stomach, PC – pyloric caeca, and MG – mid gut). P>0.05 values identify no change in the bacterial group, p<0.05 identifies decrease (Est is negative), and p<0.05 identifies increase (Est is positive) in the relative abundance of target group after the feed change. Bold values identify similarities between SalmoSim and real salmon samples. The SalmoSim values used for this test involves stable SalmoSim time points: days 16, 18 and 20 (Fish meal diet – once bacterial communities adapted to the SalmoSim environment), and days 36, 38 and 40 (Fish meal free diet – once bacterial communities adapted to feed change).