Fig. 4 | Nature Communications

Fig. 4

From: Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

Fig. 4

Intragenomic 16S gene polymorphisms in human gut microbiome isolates. a Location of SNPs present in the 16S genes of individually cultured bacterial isolates. SNP locations were identified through phasing full-length 16S gene sequences generated for each individual isolate. X-axis denotes position along the 16S gene. Y-axis denotes individual isolates clustered based on their inferred phylogeny. Dark blue region indicates the location of a polymorphism. For clarity, a maximum of five isolates belonging to the same species are shown. For details of nucleotide substitution profiles for all sequenced isolates, see Supplementary Data 2. bd Examples of nucleotide substitution profiles showing strain-level differences between isolates identified as belonging to three bacterial species: b Shigella flexneri; c Bifidobacterium longum; d Collinsella aerofaciens. For each species, two isolate nucleotide substitution profiles are shown; however, additional examples can be found in Supplementary Data 2. Isolates were identified as belonging to the same species if their representative sequences were assigned to the same OTU when clustering at 99% sequence identity. Taxonomic identification was performed using BLAST to align representative sequences to the NCBI 16S BLAST database (see Methods). 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 the number of 16S gene copies predicted for each genome. Source data are provided as a Source Data file

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