PMC full text:
Published online 2015 Aug 21. doi:Â 10.3390/ijerph120810171
Table 2
Identification of bacteria from the basil communities I, II and III growing during BPW enrichments at 37 °C and on TSA, XLD and VRBL plates by next-generation sequencing (NGS) of the 16S rRNA gene, showing bacterial groups and genera which constituted at least 1 % of the total bacteria (rescaled to 100 %).
| Sample | Basil I, BPW 3d | Basil II, BPW 5h | Basil II, BPW 28h | Basil I, TSA | Basil II, TSA | Basil III, TSA | Basil II, VRBL | Basil III, VRBL | Basil II, XLD | Basil III, XLD |
|---|---|---|---|---|---|---|---|---|---|---|
| Total number of reads | 42,703 | 29,757 | 36,870 | 13,533 | 47,182 | 39,389 | 23,565 | 38,841 | 40,201 | 31,964 |
| Median length of reads (bp) | 509 | 494 | 500 | 503 | 502 | 496 | 500 | 496 | 499 | 503 |
| Not assigned | 1,829 | 1,985 | 2,294 | 299 | 3,839 | 378 | 114 | 712 | 226 | 198 |
| Eukaryota | 0 | 14,201 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| Bacteria (rescaled to 100% below) | 40,874 | 13,572 | 34,576 | 13,234 | 43,343 | 39,011 | 23,451 | 38,129 | 39,975 | 31,766 |
| Actinobacteria | 12% | |||||||||
| Arthrobacter | 8% | |||||||||
| Kocuria | 2% | |||||||||
| Bacteroidetes | 55% | 4% | ||||||||
| Bacteroides | 42% | |||||||||
| Macellibacteroides | 3% | |||||||||
| Parabacteroides | 11% | |||||||||
| Chryseobacterium | 3% | |||||||||
| Clostridia | 6% | 1% | ||||||||
| Clostridium | 5% | |||||||||
| Alphaproteobacteria | 5% | |||||||||
| Novosphingobium | 5% | |||||||||
| Betaproteobacteria | 6% | 3% | 2% | |||||||
| Comamonas | 5% | 2% | 2% | |||||||
| Gammaproteobacteria | 38% | 95% | 93% | 83% | 100% | 97% | 100% | 98% | 100% | 100% |
| Aeromonas | 38% | 31% | 36% | |||||||
| Alishewanella | 6% | |||||||||
| Shewanella | 1% | 1% | ||||||||
| Rheinheimera | 13% | |||||||||
| Acinetobacter | 4% | 1% | 45% | 17% | 6% | |||||
| Pseudomonas | 1% | 37% | 14% | 16% | 13% | 6% | 23% | 1% | 55% | |
| Stenotrophomonas | 1% | 1% | ||||||||
| Enterobacteriaceae | 34% | 94% | 55% | 23% | 84% | 10% | 92% | 36% | 99% | 7% |
| Aranicola | 2% | |||||||||
| Cedecea | 2% | |||||||||
| Citrobacter | 17% | 1% | 1% | 2% | ||||||
| Enterobacter | 8% | 10% | 15% | 5% | 5% | 1% | 11% | 16% | 11% | 3% |
| Erwinia | 10% | 5% | 6% | 13% | 28% | 28% | ||||
| Klebsiella | 3% | 1% | 7% | 4% | 5% | 7% | 6% | |||
| Kluyvera | 1% | 1% | 1% | 1% | 4% | 6% | ||||
| Pantoea | 2% | 70% | 21% | 3% | 61% | 1% | 41% | 7% | 45% | 1% |
| Pectobacterium | 3% | 7% | ||||||||
| Raoultella | 1% | 2% |
