TABLE 1.

Significant SCNIC modules and features across R‐values in the HIV and Great Lakes datasets ANCOM analysis of the HIV and Great Lakes datasets after using SCNIC at R‐value thresholds at 0.2, 0.4, and 0.65

HIV dataset
R‐value	New OTUs in sig. modules	New significant OTUs	Lost significant OTUs	# of significant modules	Total significant features
0.2	74	1	0	14	15
0.4	26	5	0	11	17
0.65	1	25	0	2	35

Great Lakes dataset
R‐value	New OTUs in sig. modules	New significant OTUs	Lost significant OTUs	# of significant modules	Total significant features
0.2	139	0	64	1	25
0.4	64	3	14	29	33
0.65	12	13	6	24	74

Note: MSM was used as the categorical variable for differential abundance in the HIV analysis and the Great Lakes analysis tested for taxa that differed between lakes.