1. Differential abundance of bacterial families.
Differential abundance of bacterial families. Pairwise testing by the DNA extraction method was performed using DESeq2, and the log2 fold difference was displayed (column versus rows) for selected families present in all sample matrices if their adjusted P value was <0.1 (see also Table S2 in the supplemental material). The rank abundance position for each family per sample matrix type is noted according to their regularized log abundance. The baseMean (bM) indicates the mean of negative-binomial-based normalized read counts. The pairwise comparisons based on relative abundance normalization (total-sum scaling) of the bacterial families for the different DNA isolation procedures and three sample types are available through Figshare at
Berith E. Knudsen et al. mSystems 2016; doi: /mSystems