Fig. 7

Comparisons made between the two different OTU/variant calling (either DADA2 or QIIME de novo OTU picking at 99% similarity) and the two different taxa assigment algorithms (DADA2 or QIIME using the Greengenes database). Labels are: QIIME.QIIME indicating QIIME was used for OTU picking and taxonomic assigment, QIIME.DADA2 indicating QIIME was used for OTU picking and DADA2 was used for taxonomic assignment, DADA2.QIIME indicating the DADA2 was used for sequencing error supression and QIIME was used for taxonomic assignment, and DADA2.DADA2 indicating that used for both sequencing error suppresion and taxonomic assignment. a Procrustes analysis. b A comparison of the number of OTUs identified by DADA2 (clear boxes) and QIIME de novo OTU picking at 99% similarity (shaded boxes).c Taxonomic profiles of samples grouped by treatment and bioinformatics pipeline. Only major taxa are indicated in the Figure. d Correlation analysis of relative abundances of bacterial taxa at species level. For a complete list see Additional file 3: Table S3