Table 1.
Analysis of Zymobiomics microbial community DNA standard using cpn60-based CaptureSeq, shotgun sequencing, and taxonomic marker gene amplification.
| CaptureSeq Assembly 1 | Shotgun Assembly 2 | sOTU Detected 3 | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Organism | cpn60 UT Sequence Length | OTU Detected |
Assembly Length (bp) | Sequence Identity 4 | cpn60 OTU Detected | Assembly Length (bp) | Sequence Identity |
cpn60 CaptureSeq |
16S Amplification |
| Prokaryotes | |||||||||
| Bacillus subtilis | 552 | + | 2144 | 100% | + | 873 | 100% | + | + |
| Escherichia coli | 555 | + | 1138 | 97% | + | 1208 | 99% | + | + |
| Enterococcus faecalis | 552 | + | 1235 | 100% | + | 1133 | 100% | + | + |
| Lactobacillus fermentum | 552 | + | 2165 | 100% | + | 870 | 100% | + | + |
| Listeria monocytogenes | 552 | + | 1589 | 100% | + | 811 | 99% | + | + |
| Pseudomonas aeruginosa | 555 | + | 1183 | 100% | + | 668 | 93% | + | + |
| Staphylococcus aureus | 552 | + | 1849 | 100% | + | 487 | 99% | + | + |
| Salmonella enterica | 555 | + | 1138 | 97% | + | 1366 | 100% | + | + |
| Eukaryotes | |||||||||
| Saccharomyces cerevisiae | 555 | + | 1301 | 100% | + | 384 | 94% | NF 5 | NF |
| Cryptococcus neoformans | 619 6 | + | 1435 | 100% | + | 549 | 94% | + | NF |
1 OTU defined by assembly of CaptureSeq reads using Trinity as described in Methods. 2 OTU defined by assembly of shotgun metagenomic reads using Trinity as described in Methods. 3 sOTU, sub-OTU as defined by amplicon sequence variant (ASV) analysis using deblur/DADA2 as described in Methods. 4 Sequence identity between the assembled OTU and the cpn60 sequence of the corresponding species. Contains cpn60 UT and flanking sequences. 5 NF, not found. 6 cpn60 UT of C. neoformans contains a 64 bp intron, which was found in the assembled OTU and in the ASV sequence.