Table 1 Specification of inputs and outputs of the proposed method

Input

(1) Counts per sample in X and Y of bacteria observed in two groups X and Y.

(2) Phylogenetic annotation of bacteria*.

(3) Whether the bacteria of interest is increased in either X or Y (we assume it to be Y, without loss of generality).

Option

(a) Threshold value of the correlation coefficient to be used as the edge weights of the network (default value is 0.4).

(b) Threshold p value for testing whether each bacteria increased in the group specified in input (3) (default value is 0.005).

Output

The rewiring index (QNetDiff score) of the bacteria that constitute the core of the bacterial correlation network and its associated bacteria, as well as the degree, mean abundance in each group of X and Y, and p value of the change from group X to Y.

(In addition, the list of bacteria that significantly increased from group X to Y, the list of bacteria belonging to each bacterial group unified for the elimination of false correlations, and its representative.)