We use One Codex to generate microbiome reports along with a host of other analytical and visualization tools. Here is an example of a microbiome report from One Codex.
Fig. 1 shows the rank-ordered estimated abundance of each species identified in a particular sample. One Codex will often classify organisms down to the subspecies or strain level. It is fairly common for 16S or shotgun metagenomic sequencing to identify several hundred to several thousand species in a single sample.
Fig. 2 displays estimated species abundance in Krona chart format. With Krona charts one can drill-up to higher level taxonomic classifications (Family, Order, Class, Phylum) or drill-down to lower level classifications (Genus, Species, Subspecies, Strain) depending on one’s research goals.
Fig. 3 shows a species list in Linnean taxonomic tree format. A high level of biodiversity is clearly evident in this form.
As shown in Fig. 4, One Codex can be used to compare species diversity in multiple samples. Note the species relative abundance in a low-diversity sample (left) vs. a high-diversity sample (right).
Individual One Codex reports are available for each sample in a multiplexed run, thus allowing you to compare species diversity and composition between samples. We deliver One Codex reports for all microbiome and metagenomic sequencing runs.