Table 2. Number of OTUs and relative proportions (i.e., percentages of 16S rRNA gene sequences) of the most abundant phyla.
| Approach | OTUs | Singletons | Firmicutes | Bacteroidetes | Proteobacteria | Verrucomicrobia | Actinobacteria | Tenericutes | Cyanobacteria |
|---|---|---|---|---|---|---|---|---|---|
| Peach study | |||||||||
| Closed97 | 758 ↓ | 114 (15%) | 50.39% | 40.84% ↑ | 6.09% ↑ | 2.37% ↑ | 0.072% ↑ | 0.128% ↓ | 0.065% ↓ |
| Closed99 | 1,074 | 192 (18%) | 52.35% ↑ | 39.31% | 5.77% | 2.23% | 0.069% | 0.148% | 0.077% |
| De novo | 1,549 | 147 (9%) | 50.14% ↓ | 35.95% | 4.28% ↓ | 1.67% ↓ | 0.042% | 1.766% | 0.112% |
| Open97 | 1,603 | NA | 50.18% | 35.15% ↓ | 4.29% | 1.73% | 0.040% ↓ | 1.766% | 0.113% ↑ |
| Open99 | 1,680 ↑ | NA | 50.15% | 39.95% | 4.29% | 1.73% | 0.042% | 1.775% ↑ | 0.112% |
| SD: | 0.88 | 2.45 ↑ | 0.85 | 0.31 | 0.02 ↓ | 0.85 | 0.02 | ||
| Wheat study | |||||||||
| Closed97 | 1,302 ↓ | 414 (32%) | 45.81% ↓ | 32.52% | 13.41% ↑ | 5.89% ↑ | 2.25% ↓ | 0.0249% | 0.0282% ↓ |
| Closed99 | 2,008 | 734 (37%) | 65.97% ↑ | 21.29% ↓ | 7.64% | 2.06% | 2.90% | 0.0161% ↓ | 0.0456% |
| De novo | 37,474 ↑ | 28,466 (76%) | 57.96% | 31.82% | 3.18% ↓ | 0.81% ↓ | 3.46% | 0.3405% | 0.0927% |
| Open97 | 8,686 | NA | 58.73% | 32.78% | 3.22% | 0.85% | 3.53% ↑ | 0.3471% | 0.0912% |
| Open99 | 9,013 | NA | 58.73% | 32.79% ↑ | 3.21% | 0.85% | 3.53% ↑ | 0.3476% ↑ | 0.0908% |
| SD: | 6.51 ↑ | 4.53 | 4.19 | 2.03 | 0.52 | 0.17 | 0.03 ↓ | ||
| Quinoa study | |||||||||
| Closed97 | 1,062 ↓ | 333 (31%) | 55.34% ↓ | 30.29% ↑ | 4.68% ↑ | 7.20% ↑ | 2.20% ↓ | 0.051% | 0.050% |
| Closed99 | 1,606 | 578 (36%) | 69.77% ↑ | 21.32% ↓ | 2.73% | 3.29% | 2.61% | 0.045% ↓ | 0.070% ↑ |
| De novo | 17,046 ↑ | 11,500 (67%) | 63.70% | 27.53% | 2.45% ↓ | 1.04% ↓ | 3.30% | 0.280% ↑ | 0.041% |
| Open97 | 5,774 | NA | 64.08% | 28.18% | 2.46% | 1.07% | 3.35% | 0.275% | 0.037% |
| Open99 | 5,976 | NA | 64.07% | 28.17% | 2.46% | 1.07% | 3.36% ↑ | 0.275% | 0.035% ↓ |
| SD: | 4.62 ↑ | 3.04 | 0.89 | 2.49 | 0.49 | 0.12 | 0.01 ↓ | ||
| Barley study | |||||||||
| Closed97 | 1,078 ↓ | 342 (32%) | 53.50% ↓ | 32.38% | 5.09% ↑ | 6.63% ↑ | 2.29% ↓ | 0.0157% | 0.022% ↓ |
| Closed99 | 1,586 | 572 (36%) | 62.54% ↑ | 29.04% ↓ | 3.01% | 2.67% | 2.60% | 0.0131% ↓ | 0.053% |
| De novo | 15,599 ↑ | 10,429 (67%) | 55.65% | 36.03% | 2.08% | 1.20% ↓ | 3.25% | 0.2859% | 0.106% ↑ |
| Open97 | 5,366 | NA | 55.86% | 36.75% | 2.07% | 1.23% | 3.32% | 0.2809% | 0.104% |
| Open99 | 5,594 | NA | 55.85% | 36.77% ↑ | 2.06% ↓ | 1.23% | 3.32% ↑ | 0.2812% | 0.102% |
| SD: | 3.09 | 3.14 ↑ | 1.21 | 2.17 | 0.45 | 0.14 | 0.04 ↓ | ||
| Cherry study | |||||||||
| Closed97 | 2,439 ↓ | 1,942 (80%) | 50.89% | 36.60% | 6.75% ↑ | 4.67% | 0.180% | 0.000% ↓ | 0.000% ↓ |
| Closed99 | 4,217 | 3,226 (77%) | 51.68% ↑ | 36.00% ↓ | 6.18% | 5.11% ↑ | 0.172% ↓ | 0.012% | 0.001% |
| De novo | 138,203 ↑ | 64,000 (46%) | 47.27% ↓ | 43.20% ↑ | 4.80% | 3.46% | 0.208% | 0.079% | 0.002% |
| Open97 | 69,658 | NA | 48.53% | 41.71% | 4.73% ↓ | 2.90% ↓ | 0.208% | 0.096% ↑ | 0.002% ↑ |
| Open99 | 70,886 | NA | 48.53% | 41.75% | 4.73% ↓ | 2.90% ↓ | 0.209% ↑ | 0.001% | 0.002% |
| SD: | 1.68 | 3.12 ↑ | 0.90 | 0.98 | 0.02 | 0.05 | 0.00 ↓ | ||
| Raspberry study | |||||||||
| Closed97 | 2,751 ↓ | 722 (26%) | 44.99% ↓ | 40.66% ↑ | 13.33% ↑ | 0.052% ↑ | 0.092% | 0.002% ↓ | 0.001% ↓ |
| Closed99 | 4,433 | 1,231 (28%) | 45.13% | 40.53% | 13.32% | 0.052% ↑ | 0.092% | 0.002% ↓ | 0.001% ↓ |
| De novo | 92,486 ↑ | 69,306 (75%) | 46.13% ↑ | 39.40% ↓ | 12.90% ↓ | 0.049% ↓ | 0.097% ↑ | 0.005% ↑ | 0.002% ↑ |
| Open97 | 21,243 | NA | 46.10% | 39.73% | 12.99% | 0.049% ↓ | 0.088% ↓ | 0.004% | 0.001% ↓ |
| Open99 | 21,834 | NA | 46.10% | 39.72% | 12.99% | 0.049% ↓ | 0.088% ↓ | 0.004% | 0.001% ↓ |
| SD: | 0.55 | 0.56 ↑ | 0.19 | 0.002 | 0.004 | 0.001 | 0.0004 ↓ | ||
| Apple study | |||||||||
| Closed97 | 2,095 ↓ | 510 (24%) | 55.32% ↓ | 39.17% ↑ | 3.48% ↓ | 0.499% | 0.270% | 0.002% ↓ | 0.542% ↑ |
| Closed99 | 3,363 | 907 (27%) | 55.43% | 38.74% | 3.97% ↑ | 0.510% ↑ | 0.246% ↓ | 0.002% ↓ | 0.448% |
| De novo | 153,681 ↑ | 81,032 (53%) | 61.48% | 28.63% ↓ | 3.89% | 0.279% ↓ | 0.432% | 1.517% | 0.361% |
| Open97 | 69,010 | NA | 61.84% ↑ | 29.28% | 3.96% | 0.282% | 0.435% | 1.578% ↑ | 0.364% |
| Open99 | 70,056 | NA | 61.83% | 29.61% | 3.96% | 0.282% | 0.436% | 1.577% | 0.364% |
| SD: | 3.25 | 5.14 ↑ | 0.19 | 0.12 | 0.09 | 0.79 | 0.07 ↓ | ||
Notes.
The symbols (↑) and (↓) are used for the highest and the lowest value of each dataset, respectively. As explained in the main text, closed97 and closed99 refer to the closed OTU picking approach using the reference OTUs clustered at 97% (99,322 sequences) and 99% similarity (203,442 sequences), respectively. All these results were obtained using the default 97% in the similarity option of the pick_otus script (more on this in “Similarity percentage between 16S rRNA gene sequences” in Supplemental Information). The relative abundance of each phyla includes singletons and possible chimeras (see main text for more information about this). SD: standard deviation across all five OTU picking approaches.