Fig. 5

Cas-16S-seq efficiently and specifically mitigated mitochondrial 16S rRNA gene fractions in rice root microbiota profiling. Three biological replicates (Root_1–Root_3) and two technique replicates (8 and 15 index PCR cycles) were performed for each mt-gRNA treatment and control. The OTU table was rarefied to 41,500 reads per sample. a Comparison of rice mitochondrial 16S rRNA gene contents in Cas-16S-seq and regular 16S-seq (CK) sequencing results. The host 16S rRNA gene was drastically reduced after Cas9 treatment with 3 mt-gRNAs. ***ANOVA, p = 5e−16. b Rarefaction curve of Cas-16S-seq and regular 16S-seq data. The rarefaction analysis result using the data from one technique repeat (8 cycles) is shown here. c Cas-16S-seq observed more OTUs with average count per sample > 1 than regular 16S-seq. ***ANOVA, p = 4.35e−10 (see also Additional file 4: Table S6). d Analysis of differential bacterial OTUs between Cas-16S-seq and regular 16S-seq (CK). No OTU was significantly reduced in relative abundance after Cas9/gRNA treatments in all comparisons (Cas-16S-seq vs regular 16S-seq). In contrast, 29 OTUs were significantly increased in the Cas-16S-seq data (indicated by red dots; Wald test, p < 0.01; see also Additional file 4: Table S6). e Composition of bacterial communities at the phylum level. Bacterial phyla with relative abundances > 1% were shown here