TABLE 1.
Composition of the simulated sequence dataset.
| Species | Super-Kingdom | Category | Rationale | Number Reads |
| Bacteroides fragilis | Bacteria | Opportunistic pathogen | Analogous to wet-lab proficiency test mock community | 20,000 |
| Burkholderia pseudomallei | Bacteria | Pathogen | Burkholderiaceae also found in real smoked salmon sample | 8,000 |
| Escherichia coli | Bacteria | Pathogen | Analogous to wet-lab proficiency test mock community, also found in real smoked salmon sample | 80,000 |
| Salmonella enterica | Bacteria | Pathogen | Analogous to wet-lab proficiency test mock community | 125,000 |
| Fusobacterium nucleatum | Bacteria | Opportunistic pathogen | Analogous to wet-lab proficiency test mock community | 40,000 |
| Lactobacillus acidophilus | Bacteria | Background | Food additive | 175,000 |
| Lactobacillus delbrueckii | Bacteria | Background | 25,000 | |
| Listeria monocytogenes | Bacteria | Pathogen | Frequently found as food contamination | 10,000 |
| Mycobacterium colombiense | Bacteria | Opportunistic pathogen | Mycobacteria with increasing impact as food spoilage | 2,000 |
| Pseudomonas libanensis | Bacteria | Background | P. libanensis previously detected in food; Pseudomonadaceae also found in real smoked salmon sample | 200 |
| Anisakis berlandi | Eukaryota | Pathogen | Analogous to Cryptosporidium parvum from wet-lab proficiency test mock community | 1,212 |
| Anisakis brevispiculata | Eukaryota | Pathogen | 246 | |
| Anisakis paggiae | Eukaryota | Pathogen | 248 | |
| Anisakis pegreffii | Eukaryota | Pathogen | 2,051 | |
| Anisakis physeteris | Eukaryota | Pathogen | 262 | |
| Anisakis simplex | Eukaryota | Pathogen | 6,044 | |
| Anisakis typica | Eukaryota | Pathogen | 247 | |
| Aspergillus flavus | Eukaryota | Opportunistic pathogen | Analogous to Saccharomyces cerevisiae from wet-lab proficiency test mock community, toxin producer | 5,000 |
| Danio rerio | Eukaryota | Database misclassification | 4,310 | |
| Brugia malayi | Eukaryota | 64 | ||
| Caenorhabditis remanei | Eukaryota | 193 | ||
| Scomber japonicus | Eukaryota | 181 | ||
| Oncorhynchus mykiss | Eukaryota | Food | O. mykiss EST data as host background | 9,451,675 |
| African swine fever virus (ASFV) | Viruses | Run contamination | DNA virus; barcode mis-alignment/index swapping on Illumina MiSeq | 15 |
| Norwalk virus | Viruses | Pathogen | RNA virus; typical food contaminant | 946 |
| Escherichia virus phiX174 (phiX174) | Viruses | Run contamination | Barcode mis-alignment/index swapping on Illumina MiSeq | 735 |
| Aspergillus foetidus dsRNA mycovirus (AfdsV) | Viruses | Background | Model for virus of the contaminant Aspergillus flavus | 107 |
| Sum | 9,958,736 | |||