Figure 5.

Fragment length and damage rates among bacterial taxa within calculus. (a) Fragment length distribution of 50 high frequency species-level bacteria among all dental calculus grouped into three metadata categories: gram status, the presence or absence of a surface layer (S-layer), and the overall genomic GC content of the organism as documented from the reference genome in the NCBI database. Input was normalized to 400 randomly chosen reads per sample per species to mitigate the impact of sample specific read length profiles. No detectable differences in the median are apparent for the presence of an S-layer or gram status. Genomic GC content, however, does impact the overall fragment length profile of reads. (b) Deviation of the median fragment length from overall sample median fragment length of a subset of 20 oral bacteria in dental calculus colored by dataset origin. Again, genomic GC content appears to impact the fragment length profiles of individual taxa where high GC content species have shorter overall fragment length profiles. (c) Terminal cytosine damage rates (C to T substitution ratio at the first position of the 5′ end of the molecule) among 50 bacterial species in dental calculus grouped by gram status, presence or absence of an S-layer, and overall genomic GC content. No detectable differences in damage rates could be detected in any of the three chosen metadata categories. (d) Terminal cytosine damage rates (C to T substitution ratio at the first position of the 5′ end of the molecule) among 20 oral bacteria. While some differences in damage patterns can be detected, it is unclear if this is random or due to some process not examined in this study.