TABLE 2.
Results of MinION R9.4 Rev D direct metatranscriptome RNA-seq and RT-PCR amplicon sequencing, as well as NGS iSeq 100 i1 system for BHI and LJE samples collected from 4-hour and 24-hour culture with different initial growth concentration via different bioinformatic pipelines∗.
| Sequencing | Sample | Bioinformatic pipeline | ||||||||||
| MinKNOW/EPI2ME | MG-RAST | MEGAN | MEGAN-rRNA excluded | Galaxy and NCBI BLAST | ||||||||
| Taxon | Cumulative reads | Taxon | Cumulative reads | Taxon | Percentage | Taxon | Percentage | Taxon | Cumulative reads | |||
| Oxford Nanopore sequencing | Direct metatran scriptome RNA-seq | BHI-24h | Bacillus | 65,746 (37.6%) | Listeria | 75,562 (85.28%) | Bacillus | 63.6% | Listeria | 91.1% | − | − |
| Listeria | 54,140 (31.0%) | Escherichia | 4,560 (5.15%) | Listeria | 29.5% | Escherichia | 5.4% | − | − | |||
| Escherichia | 29,312 (16.8%) | Salmonella | 1,281 (1.45%) | Escherichia | 4.5% | Salmonella | 3.6% | − | − | |||
| Lactobacillus | 10,718 (6.1%) | Coptotermes | 1,237 (1.40%) | Salmonella | 2.3% | − | − | − | − | |||
| Staphylococcus | 8,772 (5.0%) | Bacillus | 952 (1.07%) | − | − | − | − | − | − | |||
| Salmonella | 6,155 (3.5%) | Tetragenococcus | 435 (0.49%) | − | − | − | − | − | − | |||
| LJE-24h | Bacillus | 25,434 (34.5%) | Listeria | 66,776 (76.55%) | Bacillus | 63.6% | Listeria | 67.5% | − | − | ||
| Escherichia | 23,084 (31.3%) | Escherichia | 9,287 (10.65%) | Listeria | 29.5% | Escherichia | 20.0% | − | − | |||
| Listeria | 16,751 (22.7%) | Salmonella | 1,849 (2.12%) | Escherichia | 4.5% | Salmonella | 12.5% | − | − | |||
| Salmonella | 4,943 (6.7%) | Bacillus | 1,028 (1.18%) | Salmonella | 2.3% | − | − | − | − | |||
| Edwardsiella | 3,515 (4.8%) | Lactobacillus | 728 (0.83%) | − | − | − | − | − | − | |||
| RT-PCR amplicon | BHI-4h | Escherichia | 5,770 (84.7%) | Escherichia | 1,342 (70.19%) | − | − | − | − | − | − | |
| Salmonella | 931 (13.7%) | Salmonella | 474 (24.79%) | − | − | − | − | − | − | |||
| Listeria | 113 (1.7%) | Enterobacter | 43 (2.25%) | − | − | − | − | − | − | |||
| − | − | Listeria | 20 (1.05%) | − | − | − | − | − | − | |||
| LJE-4h | Escherichia | 77,437 (50.9%) | Escherichia | 1,852 (88.11%) | − | − | − | − | − | − | ||
| Salmonella | 66,098 (43.4%) | Listeria | 179 (8.52%) | − | − | − | − | − | − | |||
| Listeria | 8,711 (5.7%) | Enterobacter | 45 (2.14%) | − | − | − | − | − | − | |||
| Illumina Next generation sequencing | Direct metatran scriptome RNA-seq | BHI-24h | - | − | Listeria | 163,627 (91.8%) | - | − | - | − | Escherichia | 19,207 (52.8%) |
| - | − | Escherichia | 13,706 (7.7%) | - | − | - | − | Listeria | 9,817 (27.0%) | |||
| - | − | Salmonella | 899 (0.5%) | - | − | - | − | Salmonella | 7,339 (20.2%) | |||
| LJE-24h | - | − | Listeria | 153,815 (92.9%) | - | − | - | − | Escherichia | 18,387 (54.4%) | ||
| - | − | Escherichia | 9,988 (6.0%) | - | − | - | − | Listeria | 9,136 (27.0%) | |||
| - | − | Salmonella | 1,732 (1.0%) | - | − | - | − | Salmonella | 6,279 (18.6%) | |||
∗Bold indicates the optimal bioinformatics pipeline without miss-identification.