Fig. 2

Taxa that persist and those that are differentially abundant. a Core microbiome analyses that persist in 85% of the samples for different production systems (day 7 and day 30). In the heat maps, the OTUs are sorted by their abundances with those on the top being low abundant, whereas those at the bottom are highly abundant. b Differential heat tree with taxonomy key given in the middle, and the branches where they are upregulated are coloured according to their respective categories shown on top of each subpanel