PMC full text:
Published online 2015 Aug 21. doi:Â 10.3390/ijerph120810171
Table 3
Identification of bacteria from the basil communities IV and V before, after 4 days and after 14 days of storage at 7 °C, 15 °C and 22 °C 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 IV Day0 | Basil IV 7d 4°C | Basil IV 7d 14°C | Basil IV 15d 4°C | Basil IV 15d 14°C | Basil IV 22d 4°C | Basil IV 22d 14°C | Basil V Day0 | Basil V 7d 4°C | Basil V 7d 14°C | Basil V 15d 4°C | Basil V 15d 14°C | Basil V 22d 4°C | Basil V 22d 14°C |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total number of reads | 36.746 | 35.279 | 63.993 | 11.892 | 24.615 | 49.852 | 49.347 | 60.524 | 57.824 | 83.574 | 37.559 | 51.080 | 70.829 | 64.761 |
| Median length of reads (bp) | 438 | 456 | 404 | 437 | 405 | 464 | 393 | 417 | 459 | 402 | 437 | 457 | 453 | 393 |
| Not assigned | 56 | 40 | 354 | 109 | 788 | 32 | 700 | 94 | 90 | 928 | 181 | 151 | 208 | 3.815 |
| Eukaryota | 35.626 | 34.556 | 26.747 | 9.870 | 51 | 49.363 | 222 | 46.475 | 53.834 | 1.735 | 27.767 | 48.859 | 56.755 | 9.132 |
| Bacteria (rescaled to 100 % below) | 1.065 | 682 | 36.892 | 1.913 | 23.776 | 457 | 48.425 | 13.954 | 3.900 | 80.911 | 9.611 | 2.070 | 13.867 | 51.815 |
| Actinobacteria | 14% | 1% | 1% | 14% | 1% | |||||||||
| Microbacterium | 2% | 1% | ||||||||||||
| Arthrobacter | 10% | 1% | 8% | |||||||||||
| Bacteroidetes | 4% | 2% | 17% | 29% | 18% | 14% | 16% | 19% | ||||||
| Chryseobacterium | 2% | 1% | 11% | 3% | 1% | |||||||||
| Flavobacterium | 2% | 17% | 25% | 1% | 3% | |||||||||
| Pedobacter | 2% | 18% | 2% | |||||||||||
| Sphingobacterium | 9% | 18% | ||||||||||||
| Bacilli | 2% | 1% | ||||||||||||
| Bacillus | 2% | |||||||||||||
| Clostridia | 3% | |||||||||||||
| Clostridium | 2% | |||||||||||||
| Alphaproteobacteria | 5% | 20% | 8% | 11% | 21% | 8% | 2% | 8% | 2% | 23% | 4% | 8% | ||
| Methylobacterium | 9% | 1% | ||||||||||||
| Agrobacterium | 1% | 1% | 8% | 1% | ||||||||||
| Rhizobium | 2% | 2% | 1% | 2% | 2% | |||||||||
| Novosphingobium | 5% | 19% | 4% | 6% | 8% | 3% | 2% | 7% | 1% | 11% | 3% | 3% | ||
| Sphingomonas | 1% | 1% | 1% | 1% | 1% | |||||||||
| Betaproteobacteria | 28% | 15% | 2% | 9% | 15% | 36% | 20% | 6% | 28% | |||||
| Achromobacter | 3% | 1% | 1% | |||||||||||
| Burkholderia | 2% | 1% | 1% | |||||||||||
| Acidovorax | 5% | |||||||||||||
| Comamonas | 1% | 1% | ||||||||||||
| Delftia | 1% | 8% | ||||||||||||
| Variovorax | 2% | |||||||||||||
| Duganella | 1% | 3% | ||||||||||||
| Herbaspirillum | 5% | 2% | 6% | |||||||||||
| Herminiimonas | 1% | |||||||||||||
| Janthinobacterium | 17% | 1% | 2% | 2% | ||||||||||
| Oxalicibacterium | 1% | 2% | 5% | |||||||||||
| Methylobacillus | 12% | |||||||||||||
| Methylophilus | 2% | 4% | 32% | 4% | ||||||||||
| Zoogloea | 2% | |||||||||||||
| Gammaproteobacteria | 66% | 44% | 94% | 64% | 44% | 7% | 54% | 97% | 91% | 100% | 97% | 54% | 95% | 45% |
| Pseudoalteromonas | 3% | 1% | ||||||||||||
| Acinetobacter | 4% | |||||||||||||
| Pseudomonas | 56% | 30% | 71% | 42% | 10% | 3% | 22% | 96% | 85% | 95% | 95% | 44% | 89% | 24% |
| Luteibacter | 1% | 6% | 1% | |||||||||||
| Stenotrophomonas | 1% | 22% | 2% | 17% | 4% | 12% | ||||||||
| Xanthomonas | 1% | 2% | 1% | |||||||||||
| Enterobacteriaceae | 8% | 7% | 22% | 21% | 5% | 10% | 1% | 6% | 3% | 2% | 5% | 5% | 8% | |
| Buchnera | 2% | |||||||||||||
| Enterobacter | 3% | 3% | 2% | 7% | 1% | 6% | ||||||||
| Erwinia | 3% | |||||||||||||
| Ewingella | 4% | 11% | ||||||||||||
| Pantoea | 4% | 1% | 1% | 5% | 2% | 1% | 5% | 3% | 1% | |||||
| Rahnella | 4% | 10% | 5% | 1% | 1% | |||||||||
| Serratia | 5% | 1% | ||||||||||||
| Unclassified | 2% |
