Table 1.
Overview of Illumina MiSeq sequencing by bioinformatic processing and PacBio SMRT sequencing.
| Illumina Miseq | PacBio SMRT | ||
|---|---|---|---|
| saliva | tooth biofilm | tooth biofilm | |
| Sample number | 64 | 49 | 42 |
| Mean sequence length (bp) | 429 | 424 | 1,360 |
| ProbeSeq/SMRT specific pipeline | |||
| Total number of reads | 7,858,135 | 1,328,722 | 158,705 |
| Quality filtered reads | 4,547,033 | 982,980 | 142,912 |
| Reads per sample, mean (min-max) | 71,047 (46,109–156,263) | 20,056 (8,242–34,339) | 3,367 (667–8,162) |
| Phyla1 | 10 | 10 | 10 |
| Genera1 | 98 | 86 | 77 |
| Species/phylotypes/Genus probes1 | 395 | 373 | 345 |
| QIIME | |||
| Total number of reads after filtering2 | 8,245,243 | 1,582,139 | — |
| Quality filtered reads | 5,501,208 | 1,299,986 | — |
| Reads per sample, mean (min-max) | 85,952 (60,035–180,901) | 26,526 (12,157–49,024) | — |
| Phyla1 | 10 | 10 | — |
| Genera1 | 97 | 80 | — |
| Species/phylotypes1 | 405 | 368 | — |
1For ProbeSeq and QIIME, OTUs with <10 sequences per OUT were excluded and for PacBio SMRT those with <2 sequences per OUT. 2After split library using default QIIME parameters.