Figure 4.

Differential abundance analysis

Differential abundance of families between sub-cultivations and contents for (A) chips and (B) chambers, respectively; (C) differential abundance of chip sub-cultivation versus traditional cultivation; and (D) chamber sub-cultivation and traditional cultivation. Differential abundance was determined by using DESeq2 to identify ASVs showing significant differences in abundance between cultivation strategies. Their relative abundance was then aggregated on the family level with fold-change estimates used to quantify the magnitude of these differences.