Fig. 3
From: Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Detecting Bacteroides in human stool samples. a The relative abundance of the genus Bacteroides in four human stool samples quantified using either V1–V9 amplicons (x-axis) or V1–V3 amplicons (y-axis). b The relative abundance of Bacteroides species in the same four samples. Species abundance was quantified from mWGS sequencing or from V1–V3/V1–V9 OTUs generated at 99% identity. Abundance is shown for the most abundant species as quantified by mWGS (for abundance estimates of all Bacteroides species detected by each platform, see Supplementary Table 5). c Nucleotide substitution profiles generated by aligning all V1–V9 amplicon sequences assigned to the single OTU identified as Bacteroides vulgatus. Profiles are shown for the two stool samples with high B. vulgatus relative abundance (IronHorse and Scott). d Nucleotide substitution profiles predicted from the reference genomes of two different B. vulgatus strains ATCC 848239 and mpk40. In both c and d, nucleotide substitutions were identified relative to a single reference 16S gene for B. vulgatus ATCC 8482 (NCBI Gene ID 5304800). Gray panels depict variable regions defined by commonly used primer-binding sites (Supplementary Table 1). Dashed lines indicate the expected proportion of nucleotide substitutions, given there are seven 16S gene copies within each genome. Source data are provided as a Source Data file
